Sample records for chromosome sorting

  1. Flow karyotyping and sorting of human chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Gray, J.W.; Lucas, J.; Peters, D.; Pinkel, D.; Trask, B.; van den Engh, G.; Van Dilla, M.A.


    Flow cytometry and sorting are becoming increasingly useful as tools for chromosome classfication and for the detection of numerical and structural chromosome aberrations. Chromosomes of a single type can be purified with these tools to facilitate gene mapping or production of chromosome specific recombinant DNA libraries. For analysis of chromosomes with flow cytometry, the chromosomes are extracted from mitotic cells, stained with one or more fluorescent dyes and classified one-by-one according to their dye content(s). Thus, the flow approach is fundamentally different than conventional karyotyping where chromosomes are classified within the context of a metaphase spread. Flow sorting allows purification of chromosomes that can be distinguished flow cytometrically. The authors describe the basic principles of flow cytometric chromosome classification i.e. flow karyotyping, and chromosome sorting and describe several applications. 30 refs., 8 figs.

  2. Chromosome analysis and sorting using flow cytometry. (United States)

    Doležel, Jaroslav; Kubaláková, Marie; Cíhalíková, Jarmila; Suchánková, Pavla; Simková, Hana


    Chromosome analysis and sorting using flow cytometry (flow cytogenetics) is an attractive tool for fractionating plant genomes to small parts. The reduction of complexity greatly simplifies genetics and genomics in plant species with large genomes. However, as flow cytometry requires liquid suspensions of particles, the lack of suitable protocols for preparation of solutions of intact chromosomes delayed the application of flow cytogenetics in plants. This chapter outlines a high-yielding procedure for preparation of solutions of intact mitotic chromosomes from root tips of young seedlings and for their analysis using flow cytometry and sorting. Root tips accumulated at metaphase are mildly fixed with formaldehyde, and solutions of intact chromosomes are prepared by mechanical homogenization. The advantages of the present approach include the use of seedlings, which are easy to handle, and the karyological stability of root meristems, which can be induced to high degree of metaphase synchrony. Chromosomes isolated according to this protocol have well-preserved morphology, withstand shearing forces during sorting, and their DNA is intact and suitable for a range of applications.

  3. Construction of BAC Libraries from Flow-Sorted Chromosomes. (United States)

    Šafář, Jan; Šimková, Hana; Doležel, Jaroslav


    Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

  4. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

    Directory of Open Access Journals (Sweden)

    Bartoš Jan


    Full Text Available Abstract Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA. Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which

  5. High resolution FISH on super-stretched flow-sorted plant chromosomes.

    NARCIS (Netherlands)

    Valárik, M.; Bartos, J.; Kovarova, P.; Kubalakova, M.; Jong, de J.H.S.G.M.; Dolezel, J.


    A novel high-resolution fluorescence in situ hybridisation (FISH) strategy, using super-stretched flow-sorted plant chromosomes as targets, is described. The technique that allows longitudinal extension of chromosomes of more than 100 times their original metaphase size is especially attractive for

  6. Karyotyping human and mouse cells using probes from single-sorted chromosomes and open source software. (United States)

    Potapova, Tamara A; Unruh, Jay R; Box, Andrew C; Bradford, William D; Seidel, Christopher W; Slaughter, Brian D; Sivagnanam, Shamilene; Wu, Yuping; Li, Rong


    Multispectral karyotyping analyzes all chromosomes in a single cell by labeling them with chromosome-specific probes conjugated to unique combinations of fluorophores. Currently available multispectral karyotyping systems require the purchase of specialized equipment and reagents. However, conventional laser scanning confocal microscopes that are capable of separating multiple overlapping emission spectra through spectral imaging and linear unmixing can be utilized for classifying chromosomes painted with multicolor probes. Here, we generated multicolor chromosome paints from single-sorted human and mouse chromosomes and developed the Karyotype Identification via Spectral Separation (KISS) analysis package, a set of freely available open source ImageJ tools for spectral unmixing and karyotyping. Chromosome spreads painted with our multispectral probe sets can be imaged on widely available spectral laser scanning confocal microscopes and analyzed using our ImageJ tools. Together, our probes and software enable academic labs with access to a laser-scanning spectral microscope to perform multicolor karyotyping in a cost-effective manner.

  7. Construction of BAC libraries from flow-sorted chromosomes


    Šafář, J.; Šimková, H; Doležel, J


    Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by construct...


    NARCIS (Netherlands)



    A method combining flow sorting and molecular cytogenetic techniques for the identification of unknown marker chromosomes is described. In this study, the bladder tumor cell line J82 was used, which was known to carry a marker chromosome of the size of chromosome 7 in every cell. From the cytogeneti

  9. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata.

    Directory of Open Access Journals (Sweden)

    István Molnár

    Full Text Available This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.

  10. Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA. (United States)

    Kichigin, Ilya G; Giovannotti, Massimo; Makunin, Alex I; Ng, Bee L; Kabilov, Marsel R; Tupikin, Alexey E; Barucchi, Vincenzo Caputo; Splendiani, Andrea; Ruggeri, Paolo; Rens, Willem; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A; Graphodatsky, Alexander S; Trifonov, Vladimir A


    Squamate reptiles show a striking diversity in modes of sex determination, including both genetic (XY or ZW) and temperature-dependent sex determination systems. The genomes of only a handful of species have been sequenced, analyzed and assembled including the genome of Anolis carolinensis. Despite a high genome coverage, only macrochromosomes of A. carolinensis were assembled whereas the content of most microchromosomes remained unclear. Most of the Anolis species have homomorphic XY sex chromosome system. However, some species have large heteromorphic XY chromosomes (e.g., A. sagrei) and even multiple sex chromosomes systems (e.g. A. pogus), that were shown to be derived from fusions of the ancestral XY with microautosomes. We applied next generation sequencing of flow sorting-derived chromosome-specific DNA pools to characterize the content and composition of microchromosomes in A. carolinensis and A. sagrei. Comparative analysis of sequenced chromosome-specific DNA pools revealed that the A. sagrei XY sex chromosomes contain regions homologous to several microautosomes of A. carolinensis. We suggest that the sex chromosomes of A. sagrei are derived by fusions of the ancestral sex chromosome with three microautosomes and subsequent loss of some genetic content on the Y chromosome.

  11. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.


    Kejnovský, E; Vrána, J; Matsunaga, S.; Soucek, P.; Siroký, J; Dolezel, J; Vyskot, B


    The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that ...

  12. Construction of a DNA library representing 15q11-13 by subtraction of two flow sorted marker chromosome-specific libraries

    Energy Technology Data Exchange (ETDEWEB)

    Blennow, E.; Werelius, B.; Nordenskjoeld, M. [Karolinska Hospital, Stockholm (Sweden)] [and others


    Constitutional extra {open_quotes}marker chromosomes{close_quotes} are found in {approx}0.5/1000 of newborns. Of these, 50% are inverted duplications of the pericentromeric region of chromosome 15, including two variants; (1) inv dup(15)(pter{yields}q11:q11{yields}pter) and (2) inv dup(15) (pter{yields}q12-13::q12-13{yields}pter). Variant (1) is found in phenotypically normal individuals, whereas variant (2) will produce a typical clinical picture including mental retardation, autism, hyperactivity and discrete dysmorphic features. Fluorescence in situ hybridization (FISH) using single copy probes from the Prader-Willi region confirms these observations as well as chromosome painting using a flow-sorted marker chromosome-specific library from a variant (1) marker, hybridized to the chromosomes of a patient with a variant (2) marker chromosome. Followingly, a flow-sorted biotinylated variant (1) library was subtracted from a non-labeled variant (2) library using magnetic beads and subsequent amplification by degenerate oligonucleotide-primed PCR (DOP-PCR). The successful result was demonstrated by using the amplified material for chromosome painting on chromosome slides from variant (1) and variant (2) patients. We have constructed a library from 15q11-13. This region contains genes producing a specific abnormal phenotype when found in a tri- or tetrasomic state. The region also contains the genes responsible for the Prader-Willi and Angelman syndromes when the paternal/maternal copy is missing, respectively. It is therefore a region where parental imprinting plays an important role. The isolated library may be used to isolate single copy clones which will allow further investigations of this region.

  13. Isolation and characterization of DNA probes from a flow-sorted human chromosome 8 library that detect restriction fragment length polymorphism (RFLP).


    Wood, S.; Starr, T V; Shukin, R J


    We have used a recombinant DNA library constructed from flow-sorted human chromosome 8 as a source of single-copy human probes. These probes have been screened for restriction fragment length polymorphism (RFLP) by hybridization to Southern transfers of genomic DNA from five unrelated individuals. We have detected six RFLPs distributed among four probes after screening 741 base pairs for restriction site variation. These RFLPs all behave as codominant Mendelian alleles. Two of the probes dete...

  14. [Effect of rye chromosomes on features of androgenesis in wheat-rye substituted lines of Triticum aestivum L. sort Saratovskaya 29/Secale cerale L. sort Onokhoiskaia and Triticale]. (United States)

    Dobrovolskaia, O B; Pershina, L A; Kravtsova, L A; Silkova, O G; Shchapova, A I


    The characteristic features of androgenesis in six wheat-rye substitution lines Triticum aestivum L. (cv. Saratovskaya 29)/Secale cereale L. (cv. Onokhoiskaya) and triticale (2n = 56) using anther culture at different concentrations of 2,4-D in the growth medium were studied. Under variable cultivation conditions, the significant effect of genotypic diversity on the variability of such androgenesis parameters as the frequency of productive anthers, the frequency of embryoid formation, and the frequency of total regenerated plantlets, was shown. It was demonstrated that chromosomes 1R, 3R, and 7R stimulated the formation of androgenous embryoids, while chromosome 5R produced an opposite effect. In triticale and substitution lines, the regeneration ability of androgenous embryoids induced by elevated 2,4-D concentrations was inhibited. Chromosome 1R of the Onokhoiskaya cultivar was suggested to contain genes suppressing regeneration of green plantlets, while chromosome 3R, conversely, stimulated their formation. Chromosomes 1R, 2R, 3R, and 7R of the Onokhoiskaya cultivar did not inhibit the spontaneous formation of androgenous hexaploids in the substitution lines.

  15. Chromosome (United States)

    Chromosomes are structures found in the center (nucleus) of cells that carry long pieces of DNA. DNA ... is the building block of the human body. Chromosomes also contain proteins that help DNA exist in ...

  16. Sorting choanoflagellates (United States)

    Marconi, Veronica I.; Miño, Gaston L.; Sparacino, Javier; Banchio, Adolfo J.; Condat, Carlos A.; Koehl, Mimi A. R.; King, Nicole; Stocker, Roman


    In freshwater environments, as well as in oceans, environmental conditions are in constant fluctuation. Some heterotrophic plankton must adapt their swimming behavior in order to survive under these conditions. In the case of the choanoflagellate, the closest animal ancestor, the ability to forage for food is given not only by its single flagellum, but also by its differentiation between fast and slow swimmers. The understanding of how these cells with different strategies to swim search for food can give us a better insight into how eukaryotes respond to different stimuli. In this work, we have designed a microfluidic device that sorts choanoflagellates by their speed. The optimal geometry was found by a numerical model using the experimentally determined motilities of each swimmer type.

  17. Molecular characterization of flow-sorted mammalian centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Hamkalo, B.A.; Henschen, A.; Parseghian, M.H. [Univ. of Calfornia, Irvine, CA (United States). Dept. of Molecular Biology and Biochemistry] [and others


    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project involved experiments directed towards developing a molecular characterization of the centromere region of mammalian chromosomes. Attempts to purify this essential chromosomal locus by conventional methods have thus far been unsuccessful. However, preliminary data obtained in collaboration with the National Flow Cytometry Resource (NFCR) showed that it is possible to purify a chromosome fragment that is present in certain cultured mouse cell lines and has all the properties expected of an intact centromere region. To begin sorting this minichromosome for the identification of proteins preferentially associated with centromere regions, standard buffers utilized in chromosome sorting were evaluated for potential effects on maintenance of chromosomal proteins during sorting. The data indicate that the presence of several buffer constituents results in the extraction of all but a few chromosomal proteins. The subsequent use of a magnesium sulfate buffer resulted in the sorting of mouse chromosomes that do not suffer a significant loss of proteins. Several DNA stains were also evaluated for causing protein dissociation, but no significant losses were observed. Although flow-sorted chromosomes have been used extensively for DNA analysis and cloning, this is a pioneering effort by the NFCR, and its collaborators, to exploit chromosome sorting capabilities for the analysis of chromosomal proteins.

  18. k -Bitonic sort

    Institute of Scientific and Technical Information of China (English)

    高庆狮; 胡玥; 刘志勇


    A k-bitonic sort which generalizes the bitonic sort is proposed. The theorem of the bitonic sort, which merges two monotonic sequences into one order sequence, is extended into the theorem of k-bitonic sort. The k-bitonic sort merges K (=2k or 2k-1) monotonic sequences into one order sequence in steps, where k=[K/2] is an integer and k≥1. The k-bitonic sort is the Batcher’s bitonic sort when k=1.

  19. Sex-sorting sperm using flow cytometry/cell sorting. (United States)

    Garner, Duane L; Evans, K Michael; Seidel, George E


    The sex of mammalian offspring can be predetermined by flow sorting relatively pure living populations of X- and Y-chromosome-bearing sperm. This method is based on precise staining of the DNA of sperm with the nucleic acid-specific fluorophore, Hoechst 33342, to differentiate between the subpopulations of X- and Y-sperm. The fluorescently stained sperm are then sex-sorted using a specialized high speed sorter, MoFlo(®) SX XDP, and collected into biologically supportive media prior to reconcentration and cryopreservation in numbers adequate for use with artificial insemination for some species or for in vitro fertilization. Sperm sorting can provide subpopulations of X- or Y-bearing bovine sperm at rates in the 8,000 sperm/s range while maintaining; a purity of 90% such that it has been applied to cattle on a commercial basis. The sex of offspring has been predetermined in a wide variety of mammalian species including cattle, swine, horses, sheep, goats, dogs, cats, deer, elk, dolphins, water buffalo as well as in humans using flow cytometric sorting of X- and Y-sperm.

  20. What is a Sorting Function?

    DEFF Research Database (Denmark)

    Henglein, Fritz


    What is a sorting function—not a sorting function for a given ordering relation, but a sorting function with nothing given? Formulating four basic properties of sorting algorithms as defining requirements, we arrive at intrinsic notions of sorting and stable sorting: A function is a sorting funct...... are derivable without compromising data abstraction. Finally we point out that stable sorting functions as default representations of ordering relations have the advantage of permitting linear-time sorting algorithms; inequality tests forfeit this possibility....

  1. Parallel sorting algorithms

    CERN Document Server

    Akl, Selim G


    Parallel Sorting Algorithms explains how to use parallel algorithms to sort a sequence of items on a variety of parallel computers. The book reviews the sorting problem, the parallel models of computation, parallel algorithms, and the lower bounds on the parallel sorting problems. The text also presents twenty different algorithms, such as linear arrays, mesh-connected computers, cube-connected computers. Another example where algorithm can be applied is on the shared-memory SIMD (single instruction stream multiple data stream) computers in which the whole sequence to be sorted can fit in the

  2. Designing sorting networks

    CERN Document Server

    Baddar, Sherenaz W Al-Haj


    Designing Sorting Networks: A New Paradigm provides an in-depth guide to maximizing the efficiency of sorting networks, and uses 0/1 cases, partially ordered sets and Haase diagrams to closely analyze their behavior in an easy, intuitive manner. This book also outlines new ideas and techniques for designing faster sorting networks using Sortnet, and illustrates how these techniques were used to design faster 12-key and 18-key sorting networks through a series of case studies. Finally, it examines and explains the mysterious behavior exhibited by the fastest-known 9-step 16-key network. Designi

  3. Sorting a distribution theory

    CERN Document Server

    Mahmoud, Hosam M


    A cutting-edge look at the emerging distributional theory of sorting Research on distributions associated with sorting algorithms has grown dramatically over the last few decades, spawning many exact and limiting distributions of complexity measures for many sorting algorithms. Yet much of this information has been scattered in disparate and highly specialized sources throughout the literature. In Sorting: A Distribution Theory, leading authority Hosam Mahmoud compiles, consolidates, and clarifies the large volume of available research, providing a much-needed, comprehensive treatment of the

  4. Cell sorting in development. (United States)

    Krens, S F Gabby; Heisenberg, Carl-Philipp


    During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes.

  5. Layers in sorting practices: Sorting out patients with potential cancer

    DEFF Research Database (Denmark)

    Møller, Naja Holten; Bjørn, Pernille


    mechanism, but is handled by informal sorting mechanisms. We identify two informal sorting mechanisms with large impact on the sorting practices, namely subtle categorizing and collective remembering. These informal sorting mechanisms have implications for the design of electronic booking systems because...

  6. LazySorted: A Lazily, Partially Sorted Python List

    Directory of Open Access Journals (Sweden)

    Naftali Harris


    Full Text Available LazySorted is a Python C extension implementing a partially and lazily sorted list data structure. It solves a common problem faced by programmers, in which they need just part of a sorted list, like its middle element (the median, but sort the entire list to get it. LazySorted presents them with the abstraction that they are working with a fully sorted list, while actually only sorting the list partially with quicksort partitions to return the requested sub-elements. This enables programmers to use naive "sort first" algorithms but nonetheless attain linear run-times when possible. LazySorted may serve as a drop-in replacement for the built-in sorted function in most cases, and can sometimes achieve run-times more than 7 times faster.

  7. Chromosomal rearrangements in cattle and pigs revealed by chromosome microdissection and chromosome painting

    Directory of Open Access Journals (Sweden)

    Yerle Martine


    Full Text Available Abstract A pericentric inversion of chromosome 4 in a boar, as well as a case of (2q-;5p+ translocation mosaicism in a bull were analysed by chromosome painting using probes generated by conventional microdissection. For the porcine inversion, probes specific for p arms and q arms were produced and hybridised simultaneously on metaphases of a heterozygote carrier. In the case of the bovine translocation, two whole chromosome probes (chromosome 5, and derived chromosome 5 were elaborated and hybridised independently on chromosomal preparations of the bull who was a carrier of the mosaic translocation. The impossibility of differentiating chromosomes 2 and der(2 from other chromosomes of the metaphases did not allow the production of painting probes for these chromosomes. For all experiments, the quality of painting was comparable to that usually observed with probes obtained from flow-sorted chromosomes. The results obtained allowed confirmation of the interpretations proposed with G-banding karyotype analyses. In the bovine case, however, the reciprocity of the translocation could not be proven. The results presented in this paper show the usefulness of the microdissection technique for characterising chromosomal rearrangements in species for which commercial probes are not available. They also confirmed that the main limiting factor of the technique is the quality of the chromosomal preparations, which does not allow the identification of target chromosomes or chromosome fragments in all cases.

  8. Ready, steady, SORT!

    CERN Multimedia

    Laëtitia Pedroso


    The selective or ecological sorting of waste is already second nature to many of us and concerns us all. As the GS Department's new awareness-raising campaign reminds us, everything we do to sort waste contributes to preserving the environment.    Placemats printed on recycled paper using vegetable-based ink will soon be distributed in Restaurant No.1.   Environmental protection is never far from the headlines, and CERN has a responsibility to ensure that the 3000 tonnes and more of waste it produces every year are correctly and selectively sorted. Materials can be given a second life through recycling and re-use, thereby avoiding pollution from landfill sites and incineration plants and saving on processing costs. The GS Department is launching a new poster campaign designed to raise awareness of the importance of waste sorting and recycling. "After conducting a survey to find out whether members of the personnel were prepared to make an effort to sort a...

  9. Sorting Plastic Waste in Hydrocyclone

    Directory of Open Access Journals (Sweden)

    Ernestas Šutinys


    Full Text Available The article presents material about sorting plastic waste in hydrocyclone. The tests on sorting plastic waste were carried out. Also, the findings received from the performed experiment on the technology of sorting plastic waste are interpreted applying an experimental model of the equipment used for sorting plastics of different density.Article in Lithuanian

  10. Wage Sorting Trends

    DEFF Research Database (Denmark)

    Bagger, Jesper; Vejlin, Rune Majlund; Sørensen, Kenneth Lykke

    Using a population-wide Danish Matched Employer-Employee panel from 1980-2006, we document a strong trend towards more positive assortative wage sorting. The correlation between worker and firm fixed effects estimated from a log wage regression increases from -0.07 in 1981 to .14 in 2001. The non......Using a population-wide Danish Matched Employer-Employee panel from 1980-2006, we document a strong trend towards more positive assortative wage sorting. The correlation between worker and firm fixed effects estimated from a log wage regression increases from -0.07 in 1981 to .14 in 2001...

  11. Sorting by Recursive Partitioning, (United States)


    asymptotic time-complexity. This paper has the following main parts: First, a Pidgin -Algol version of the algorithm is presented and we discuss the main...those sorted subsets e) end "UsingBin*; end "AdaptSorting. 4 "Figure 1: A condensed Pidgin -Algol version of Adaptsort eiFor some conditions that we will...algorithm which have to be completed in either linear or constant times (these required critical times appear as comments in the Pidgin -Algol version

  12. Gender Differences in Sorting

    DEFF Research Database (Denmark)

    Merlino, Luca Paolo; Parrotta, Pierpaolo; Pozzoli, Dario

    In this paper, we investigate the sorting of workers in firms to understand gender gaps in labor market outcomes. Using Danish employer-employee matched data, we fiend strong evidence of glass ceilings in certain firms, especially after motherhood, preventing women from climbing the career ladder...

  13. Det sorte USA

    DEFF Research Database (Denmark)

    Brøndal, Jørn

    Bogen gennemgår det sorte USAs historie fra 1776 til 2016, idet grundtemaet er spændingsforholdet mellem USAs grundlæggelsesidealer og den racemæssige praksis, et spændingsforhold som Gunnar Myrdal kaldte "det amerikanske dilemma." Bogen, der er opbygget som politisk, social og racemæssig historie...

  14. Online Sorted Range Reporting

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Greve, Mark


    We study the following one-dimensional range reporting problem: On an arrayA of n elements, support queries that given two indices i ≤ j and an integerk report the k smallest elements in the subarray A[i..j] in sorted order. We present a data structure in the RAM model supporting such queries in ...

  15. Chromosomes in the flow to simplify genome analysis. (United States)

    Doležel, Jaroslav; Vrána, Jan; Safář, Jan; Bartoš, Jan; Kubaláková, Marie; Simková, Hana


    Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.

  16. K-sort: A new sorting algorithm that beats Heap sort for n <= 70 lakhs!

    CERN Document Server

    Sundararajan, Kiran Kumar; Chakraborty, Soubhik; Mahanti, N C


    Sundararajan and Chakraborty (2007) introduced a new version of Quick sort removing the interchanges. Khreisat (2007) found this algorithm to be competing well with some other versions of Quick sort. However, it uses an auxiliary array thereby increasing the space complexity. Here, we provide a second version of our new sort where we have removed the auxiliary array. This second improved version of the algorithm, which we call K-sort, is found to sort elements faster than Heap sort for an appreciably large array size (n <= 70,00,000) for uniform U[0, 1] inputs.

  17. Chip-based droplet sorting (United States)

    Beer, Neil Reginald; Lee, Abraham; Hatch, Andrew


    A non-contact system for sorting monodisperse water-in-oil emulsion droplets in a microfluidic device based on the droplet's contents and their interaction with an applied electromagnetic field or by identification and sorting.

  18. Chip-based droplet sorting

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Lee, Abraham; Hatch, Andrew


    A non-contact system for sorting monodisperse water-in-oil emulsion droplets in a microfluidic device based on the droplet's contents and their interaction with an applied electromagnetic field or by identification and sorting.

  19. Sorting quantum systems efficiently (United States)

    Ionicioiu, Radu


    Measuring the state of a quantum system is a fundamental process in quantum mechanics and plays an essential role in quantum information and quantum technologies. One method to measure a quantum observable is to sort the system in different spatial modes according to the measured value, followed by single-particle detectors on each mode. Examples of quantum sorters are polarizing beam-splitters (PBS) – which direct photons according to their polarization – and Stern-Gerlach devices. Here we propose a general scheme to sort a quantum system according to the value of any d-dimensional degree of freedom, such as spin, orbital angular momentum (OAM), wavelength etc. Our scheme is universal, works at the single-particle level and has a theoretical efficiency of 100%. As an application we design an efficient OAM sorter consisting of a single multi-path interferometer which is suitable for a photonic chip implementation.

  20. Heideggers sorte arv

    DEFF Research Database (Denmark)

    Olesen, Søren Gosvig


    Martin Heidegger var antisemit, men er hans tænkning og intellektuelle arv det også? Søren Gosvig Olesen opsøger den store tyske tænkers arvinger og bindene fra 1938-48 i Heideggers efterladte ’Sorte hæfter’, hvor den lille mands meninger blander sig med en stor tænkers tanker......Martin Heidegger var antisemit, men er hans tænkning og intellektuelle arv det også? Søren Gosvig Olesen opsøger den store tyske tænkers arvinger og bindene fra 1938-48 i Heideggers efterladte ’Sorte hæfter’, hvor den lille mands meninger blander sig med en stor tænkers tanker...

  1. Seminal plasma affects sperm sex sorting in boars. (United States)

    Alkmin, Diego V; Parrilla, Inmaculada; Tarantini, Tatiana; Del Olmo, David; Vazquez, Juan M; Martinez, Emilio A; Roca, Jordi


    Two experiments were conducted in boar semen samples to evaluate how both holding time (24h) and the presence of seminal plasma (SP) before sorting affect sperm sortability and the ability of sex-sorted spermatozoa to tolerate liquid storage. Whole ejaculate samples were divided into three aliquots immediately after collection: one was diluted (1:1, v/v) in Beltsville thawing solution (BTS; 50% SP); the SP of the other two aliquots was removed and the sperm pellets were diluted with BTS + 10% of their own SP (10% SP) or BTS alone (0% SP). The three aliquots of each ejaculate were divided into two portions, one that was processed immediately for sorting and a second that was sorted after 24h storage at 15-17°C. In the first experiment, the ability to exhibit well-defined X- and Y-chromosome-bearing sperm peaks (split) in the cytometry histogram and the subsequent sorting efficiency were assessed (20 ejaculates). In contrast with holding time, the SP proportion influenced the parameters examined, as evidenced by the higher number of ejaculates exhibiting split and better sorting efficiency (P<0.05) in semen samples with 0-10% SP compared with those with 50% SP. In a second experiment, the quality (viability, total and progressive motility) and functionality (plasma membrane fluidity and intracellular generation of reactive oxygen species) of sex-sorted spermatozoa were evaluated after 0, 72 and 120h storage at 15-17°C (10 ejaculates). Holding time and SP proportion did not influence the quality or functionality of stored sex-sorted spermatozoa. In conclusion, a holding time as long as 24h before sorting did not negatively affect sex sorting efficiency or the ability of sorted boar spermatozoa to tolerate long-term liquid storage. A high proportion of SP (50%) in the semen samples before sorting reduced the number of ejaculates to be sorted and negatively influenced the sorting efficiency, but did not affect the ability of sex-sorted spermatozoa to tolerate liquid

  2. Spin-the-bottle Sort and Annealing Sort: Oblivious Sorting via Round-robin Random Comparisons

    CERN Document Server

    Goodrich, Michael T


    We study sorting algorithms based on randomized round-robin comparisons. Specifically, we study Spin-the-bottle sort, where comparisons are unrestricted, and Annealing sort, where comparisons are restricted to a distance bounded by a \\emph{temperature} parameter. Both algorithms are simple, randomized, data-oblivious sorting algorithms, which are useful in privacy-preserving computations, but, as we show, Annealing sort is much more efficient. We show that there is an input permutation that causes Spin-the-bottle sort to require $\\Omega(n^2\\log n)$ expected time in order to succeed, and that in $O(n^2\\log n)$ time this algorithm succeeds with high probability for any input. We also show there is an implementation of Annealing sort that runs in $O(n\\log n)$ time and succeeds with very high probability.

  3. Spin-the-bottle Sort and Annealing Sort: Oblivious Sorting via Round-robin Random Comparisons. (United States)

    Goodrich, Michael T


    We study sorting algorithms based on randomized round-robin comparisons. Specifically, we study Spin-the-bottle sort, where comparisons are unrestricted, and Annealing sort, where comparisons are restricted to a distance bounded by a temperature parameter. Both algorithms are simple, randomized, data-oblivious sorting algorithms, which are useful in privacy-preserving computations, but, as we show, Annealing sort is much more efficient. We show that there is an input permutation that causes Spin-the-bottle sort to require Ω(n(2) log n) expected time in order to succeed, and that in O(n(2) log n) time this algorithm succeeds with high probability for any input. We also show there is a specification of Annealing sort that runs in O(n log n) time and succeeds with very high probability.

  4. Deductive sort and climbing sort: new methods for non-dominated sorting. (United States)

    McClymont, Kent; Keedwell, Ed


    In recent years an increasing number of real-world many-dimensional optimisation problems have been identified across the spectrum of research fields. Many popular evolutionary algorithms use non-dominance as a measure for selecting solutions for future generations. The process of sorting populations into non-dominated fronts is usually the controlling order of computational complexity and can be expensive for large populations or for a high number of objectives. This paper presents two novel methods for non-dominated sorting: deductive sort and climbing sort. The two new methods are compared to the fast non-dominated sort of NSGA-II and the non-dominated rank sort of the omni-optimizer. The results demonstrate the improved efficiencies of the deductive sort and the reductions in comparisons that can be made when applying inferred dominance relationships defined in this paper.

  5. Selective sorting of waste

    CERN Multimedia


    Not much effort needed, just willpower In order to keep the cost of disposing of waste materials as low as possible, CERN provides two types of recipient at the entrance to each building: a green plastic one for paper/cardboard and a metal one for general refuse. For some time now we have noticed, to our great regret, a growing negligence as far as selective sorting is concerned, with, for example, the green recipients being filled with a mixture of cardboard boxes full of polystyrene or protective wrappers, plastic bottles, empty yogurts pots, etc. …We have been able to ascertain, after careful checking, that this haphazard mixing of waste cannot be attributed to the cleaning staff but rather to members of the personnel who unscrupulously throw away their rubbish in a completely random manner. Non-sorted waste entails heavy costs for CERN. For information, once a non-compliant item is found in a green recipient, the entire contents are sent off for incineration rather than recycling… We are all concerned...

  6. Marker chromosomes. (United States)

    Rao, Kiran Prabhaker; Belogolovkin, Victoria


    Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

  7. Resolving sorting mechanisms into exosomes

    NARCIS (Netherlands)

    Stoorvogel, Willem


    The complexity of mechanisms driving protein sorting into exosomes is only beginning to emerge. In a paper recently published in Cell Research, Roucourt et al. report that trimming of heparan sulfate side chains of syndecans by endosomal heparanase facilitates sorting into exosomes by the formation

  8. National flow cytometry and sorting research resource. Annual progress report, July, 1, 1994--June 30, 1995, Year 12

    Energy Technology Data Exchange (ETDEWEB)

    Jett, J.H.


    Research progress utilizing flow cytometry is described. Topics include: rapid kinetics flow cytometry; characterization of size determinations for small DNA fragments; statistical analysis; energy transfer measurements of molecular confirmation in micelles; and enrichment of Mus spretus chromosomes by dual parameter flow sorting and identification of sorted fractions by fluorescence in-situ hybridization onto G-banded mouse metaphase spreads.

  9. Automated Sorting of Transuranic Waste

    Energy Technology Data Exchange (ETDEWEB)

    Shurtliff, Rodney Marvin


    The HANDSS-55 Transuranic Waste Sorting Module is designed to sort out items found in 55-gallon drums of waste as determined by an operator. Innovative imaging techniques coupled with fast linear motor-based motion systems and a flexible end-effector system allow the operator to remove items from the waste stream by a touch of the finger. When all desired items are removed from the waste stream, the remaining objects are automatically moved to a repackaging port for removal from the glovebox/cell. The Transuranic Waste Sorting Module consists of 1) a high accuracy XYZ Stereo Measurement and Imaging system, 2) a vibrating/tilting sorting table, 3) an XY Deployment System, 4) a ZR Deployment System, 5) several user-selectable end-effectors, 6) a waste bag opening system, 7) control and instrumentation, 8) a noncompliant waste load-out area, and 9) a Human/Machine Interface (HMI). The system is modular in design to accommodate database management tools, additional load-out ports, and other enhancements. Manually sorting the contents of a 55-gallon drum takes about one day per drum. The HANDSS-55 Waste Sorting Module is designed to significantly increase the throughput of this sorting process by automating those functions that are strenuous and tiresome for an operator to perform. The Waste Sorting Module uses the inherent ability of an operator to identify the items that need to be segregated from the waste stream and then, under computer control, picks that item out of the waste and deposits it in the appropriate location. The operator identifies the object by locating the visual image on a large color display and touches the image on the display with his finger. The computer then determines the location of the object, and performing a highspeed image analysis determines its size and orientation, so that a robotic gripper can be deployed to pick it up. Following operator verification by voice or function key, the object is deposited into a specified location.

  10. Modeling Chromosomes (United States)

    Robertson, Carol


    Learning about chromosomes is standard fare in biology classrooms today. However, students may find it difficult to understand the relationships among the "genome", "chromosomes", "genes", a "gene locus", and "alleles". In the simple activity described in this article, which follows the 5E approach…

  11. Sorting and selection in posets

    DEFF Research Database (Denmark)

    Daskalakis, Constantinos; Karp, Richard M.; Mossel, Elchanan


    Classical problems of sorting and searching assume an underlying linear ordering of the objects being compared. In this paper, we study these problems in the context of partially ordered sets, in which some pairs of objects are incomparable. This generalization is interesting from a combinatorial...

  12. Swarm-Based Spatial Sorting

    CERN Document Server

    Amos, Martyn


    Purpose: To present an algorithm for spatially sorting objects into an annular structure. Design/Methodology/Approach: A swarm-based model that requires only stochastic agent behaviour coupled with a pheromone-inspired "attraction-repulsion" mechanism. Findings: The algorithm consistently generates high-quality annular structures, and is particularly powerful in situations where the initial configuration of objects is similar to those observed in nature. Research limitations/implications: Experimental evidence supports previous theoretical arguments about the nature and mechanism of spatial sorting by insects. Practical implications: The algorithm may find applications in distributed robotics. Originality/value: The model offers a powerful minimal algorithmic framework, and also sheds further light on the nature of attraction-repulsion algorithms and underlying natural processes.

  13. Sorting fluorescent nanocrystals with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Gerion, Daniele; Parak, Wolfgang J.; Williams, Shara C.; Zanchet, Daniela; Micheel, Christine M.; Alivisatos, A. Paul


    Semiconductor nanocrystals with narrow and tunable fluorescence are covalently linked to oligonucleotides. These biocompounds retain the properties of both nanocrystals and DNA. Therefore, different sequences of DNA can be coded with nanocrystals and still preserve their ability to hybridize to their complements. We report the case where four different sequences of DNA are linked to four nanocrystal samples having different colors of emission in the range of 530-640 nm. When the DNA-nanocrystal conjugates are mixed together, it is possible to sort each type of nanoparticle using hybridization on a defined micrometer -size surface containing the complementary oligonucleotide. Detection of sorting requires only a single excitation source and an epifluorescence microscope. The possibility of directing fluorescent nanocrystals towards specific biological targets and detecting them, combined with their superior photo-stability compared to organic dyes, opens the way to improved biolabeling experiments, such as gene mapping on a nanometer scale or multicolor microarray analysis.

  14. Sorting of Sperm by Morphology (United States)

    Koh, James; Marcos, Marcos


    Many studies have proven that the percentage of morphologically normal sperm is a significant factor in determining the success of assisted reproduction. The velocity of sperm in a microchannel with shear flow subjected to an external field will be explored theoretically. The difference in response between morphologically normal and abnormal sperm will be computed from a statistical approach, to study the feasibility and effectiveness of sorting by an external field to remove abnormal sperm. The full name of this author is Marcos.

  15. Sorting Techniques for Plastics Recycling

    Institute of Scientific and Technical Information of China (English)


    This paper presents the basic principles of three different types of separating methods and a general guideline for choosing the most effective method for sorting plastic mixtures. It also presents the results of the tests carried out for separation of PVC, ABS and PET from different kinds of plastic mixtures in order to improve the grade of the raw input used in mechanical or feedstock recycling.

  16. Flow cytometry and cell sorting. (United States)

    Ibrahim, Sherrif F; van den Engh, Ger


    Flow cytometry and cell sorting are well-established technologies in clinical diagnostics and biomedical research. Heterogeneous mixtures of cells are placed in suspension and passed single file across one or more laser interrogation points. Light signals emitted from the particles are collected and correlated to entities such as cell morphology, surface and intracellular protein expression, gene expression, and cellular physiology. Based on user-defined parameters, individual cells can then be diverted from the fluid stream and collected into viable, homogeneous fractions at exceptionally high speeds and a purity that approaches 100%. As such, the cell sorter becomes the launching point for numerous downstream studies. Flow cytometry is a cornerstone in clinical diagnostics, and cheaper, more versatile machines are finding their way into widespread and varied uses. In addition, advances in computing and optics have led to a new generation of flow cytometers capable of processing cells at orders of magnitudes faster than their predecessors, and with staggering degrees of complexity, making the cytometer a powerful discovery tool in biotechnology. This chapter will begin with a discussion of basic principles of flow cytometry and cell sorting, including a technical description of factors that contribute to the performance of these instruments. The remaining sections will then be divided into clinical- and research-based applications of flow cytometry and cell sorting, highlighting salient studies that illustrate the versatility of this indispensable technology.

  17. Word Sorts for General Music Classes (United States)

    Cardany, Audrey Berger


    Word sorts are standard practice for aiding children in acquiring skills in English language arts. When included in the general music classroom, word sorts may aid students in acquiring a working knowledge of music vocabulary. The author shares a word sort activity drawn from vocabulary in John Lithgow's children's book "Never Play…

  18. How does the Shift-insertion sort behave when the sorting elements follow a Normal distribution?

    CERN Document Server

    Pal, Mita; Mahanti, N C


    The present paper examines the behavior of Shift-insertion sort (insertion sort with shifting) for normal distribution inputs and is in continuation of our earlier work on this new algorithm for discrete distribution inputs, namely, negative binomial. Shift insertion sort is found more sensitive for main effects but not for all interaction effects compared to conventional insertion sort.

  19. Localization of Sry gene on Y chromosome of Muntjac munticus vaginalis

    Institute of Scientific and Technical Information of China (English)


    The chromosomes 1, Y1, Y2 of Muntjac munticus vaginalis were isolated by fluorescence activated chromosome sorting and amplified by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR). A primer pair within human Sry HMG box was designed and the Sry gene of the male M. m vaginalis was amplified. The product was cloned and sequenced. The result proved that Sry is located on chromosome Y2, which is the sex-determining chromosome in the male M. m vaginalis.

  20. Polarized sorting and trafficking in epithelial cells

    Institute of Scientific and Technical Information of China (English)

    Xinwang Cao; Michal A Surma; Kai Simons


    The polarized distribution of proteins and lipids at the surface membrane of epithelial cells results in the formation of an apical and a basolateral domain,which are separated by tight junctions.The generation and maintenance of epithelial polarity require elaborate mechanisms that guarantee correct sorting and vectorial delivery of cargo molecules.This dynamic process involves the interaction of sorting signals with sorting machineries and the formation of transport carriers.Here we review the recent advances in the field of polarized sorting in epithelial cells.We especially highlight the role of lipid rafts in apical sorting.

  1. Synthetic chromosomes. (United States)

    Schindler, Daniel; Waldminghaus, Torsten


    What a living organism looks like and how it works and what are its components-all this is encoded on DNA, the genetic blueprint. Consequently, the way to change an organism is to change its genetic information. Since the first pieces of recombinant DNA have been used to transform cells in the 1970s, this approach has been enormously extended. Bigger and bigger parts of the genetic information have been exchanged or added over the years. Now we are at a point where the construction of entire chromosomes becomes a reachable goal and first examples appear. This development leads to fundamental new questions, for example, about what is possible and desirable to build or what construction rules one needs to follow when building synthetic chromosomes. Here we review the recent progress in the field, discuss current challenges and speculate on the appearance of future synthetic chromosomes.

  2. Sorting and Selection in Posets

    CERN Document Server

    Daskalakis, Constantinos; Mossel, Elchanan; Riesenfeld, Samantha; Verbin, Elad


    Classical problems of sorting and searching assume an underlying linear ordering of the objects being compared. In this paper, we study a more general setting, in which some pairs of objects are incomparable. This generalization is relevant in applications related to rankings in sports, college admissions, or conference submissions. It also has potential applications in biology, such as comparing the evolutionary fitness of different strains of bacteria, or understanding input-output relations among a set of metabolic reactions or the causal influences among a set of interacting genes or proteins. Our results improve and extend results from two decades ago of Faigle and Tur\\'{a}n. A measure of complexity of a partially ordered set (poset) is its width. Our algorithms obtain information about a poset by queries that compare two elements. We present an algorithm that sorts, i.e. completely identifies, a width w poset of size n and has query complexity O(wn + nlog(n)), which is within a constant factor of the in...

  3. Energy efficient data sorting using standard sorting algorithms

    KAUST Repository

    Bunse, Christian


    Protecting the environment by saving energy and thus reducing carbon dioxide emissions is one of todays hottest and most challenging topics. Although the perspective for reducing energy consumption, from ecological and business perspectives is clear, from a technological point of view, the realization especially for mobile systems still falls behind expectations. Novel strategies that allow (software) systems to dynamically adapt themselves at runtime can be effectively used to reduce energy consumption. This paper presents a case study that examines the impact of using an energy management component that dynamically selects and applies the "optimal" sorting algorithm, from an energy perspective, during multi-party mobile communication. Interestingly, the results indicate that algorithmic performance is not key and that dynamically switching algorithms at runtime does have a significant impact on energy consumption. © Springer-Verlag Berlin Heidelberg 2011.

  4. Fixing the Sorting Algorithm for Android, Java and Python

    NARCIS (Netherlands)

    Gouw, C.P.T. de; Boer, F.S. de


    Tim Peters developed the Timsort hybrid sorting algorithm in 2002. TimSort was first developed for Python, a popular programming language, but later ported to Java (where it appears as java.util.Collections.sort and java.util.Arrays.sort). TimSort is today used as the default sorting algorithm in Ja

  5. Construction and characterization of genomic libraries from specific human chromosomes. (United States)

    Krumlauf, R; Jeanpierre, M; Young, B D


    Highly purified fractions of human chromosomes 21 and 22 were isolated from a suspension of metaphase chromosomes stained with ethidium bromide by using a fluorescence-activated cell sorter (FACS II). Two recombinant DNA libraries, representing chromosomes 21 and 22, were constructed by complete digestion of DNA from these fractions with EcoRI and insertion into the vector lambda gtWES lambda B. Twenty clones selected at random from the chromosome 22 library hybridized to EcoRI-digested human DNA, and five of these clones hybridized to single bands identical in size to the phage inserts. These five single-copy sequences and a clone coding for an 8S RNA isolated by screening the chromosome 22 library for expressed sequences were characterized in detail. Hybridization of all six clones to a panel of sorted chromosomes and hybrid cell lines confirmed the assignment of the sequences to chromosome 22. The sequences were localized to regions of chromosome 22 by hybridization to translocated chromosomes sorted from a cell line having a balanced translocation t(17;22)(p13;q11) and to hybrid cell lines containing the various portions of another translocation t(X;22)(q13;q112). Five clones reside on the long arm of chromosome 22 between q112 and pter, while one clone and an 18S rRNA gene isolated from the chromosome 22 library reside pter and g112. The construction of chromosome-specific libraries by this method has the advantage of being direct and applicable to nearly all human chromosomes and will be important in molecular analysis of human genetic diseases.

  6. Chromosome Analysis (United States)


    Perceptive Scientific Instruments, Inc., provides the foundation for the Powergene line of chromosome analysis and molecular genetic instrumentation. This product employs image processing technology from NASA's Jet Propulsion Laboratory and image enhancement techniques from Johnson Space Center. Originally developed to send pictures back to earth from space probes, digital imaging techniques have been developed and refined for use in a variety of medical applications, including diagnosis of disease.

  7. On the Construction of Sorted Reactive Systems

    DEFF Research Database (Denmark)

    Birkedal, Lars; Debois, Søren; Hildebrandt, Thomas


    We develop a theory of sorted bigraphical reactive systems. Every application of bigraphs in the literature has required an extension, a sorting, of pure bigraphs. In turn, every such application has required a redevelopment of the theory of pure bigraphical reactive systems for the sorting at hand...... bigraphs. Technically, we give our construction for ordinary reactive systems, then lift it to bigraphical reactive systems. As such, we give also a construction of sortings for ordinary reactive systems. This construction is an improvement over previous attempts in that it produces smaller and much more...

  8. Design and realization of sort manipulator of crystal-angle sort machine (United States)

    Wang, Ming-shun; Chen, Shu-ping; Guan, Shou-ping; Zhang, Yao-wei


    It is a current tendency of development in automation technology to replace manpower with manipulators in working places where dangerous, harmful, heavy or repetitive work is involved. The sort manipulator is installed in a crystal-angle sort machine to take the place of manpower, and engaged in unloading and sorting work. It is the outcome of combing together mechanism, electric transmission, and pneumatic element and micro-controller control. The step motor makes the sort manipulator operate precisely. The pneumatic elements make the sort manipulator be cleverer. Micro-controller's software bestows some simple artificial intelligence on the sort manipulator, so that it can precisely repeat its unloading and sorting work. The combination of manipulator's zero position and step motor counting control puts an end to accumulating error in long time operation. A sort manipulator's design in the practice engineering has been proved to be correct and reliable.

  9. Recent advances in flow cytometric cell sorting. (United States)

    Osborne, Geoffrey W


    The classification and separation of one cell type or particle from others is a fundamental task in many areas of science. Numerous techniques are available to perform this task; however, electrostatic cell sorting has gained eminence over others because, when combined with the analysis capabilities of flow cytometry it provides flexible separations based on multiple parameters. Unlike competing technologies, such as gradient or magnetic separations that offer much larger total throughput, flow cytometric cell sorting permits selections based on various levels of fluorescent reporters, rather the complete presence or absence of the reporter. As such, this technology has found application in a huge range of fields. This chapter aims to describe the utility of single-cell sorting with particular emphasis given to index sorting. This is followed by two recently developed novel techniques of sorting cells or particles. The first of these is positional sorting which is useful in cell-based studies where sorting can proceed and produce meaningful results without being inherently dependant on prior knowledge of where gates should be set. Secondly, reflective plate sorting is introduced which positionally links multiwell sample and collection plates in a convenient assay format so that cells in the collection plate "reflect" those in the sample plate.

  10. Data Sorting Using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    M. J. Mišić


    Full Text Available Graphics processing units (GPUs have been increasingly used for general-purpose computation in recent years. The GPU accelerated applications are found in both scientific and commercial domains. Sorting is considered as one of the very important operations in many applications, so its efficient implementation is essential for the overall application performance. This paper represents an effort to analyze and evaluate the implementations of the representative sorting algorithms on the graphics processing units. Three sorting algorithms (Quicksort, Merge sort, and Radix sort were evaluated on the Compute Unified Device Architecture (CUDA platform that is used to execute applications on NVIDIA graphics processing units. Algorithms were tested and evaluated using an automated test environment with input datasets of different characteristics. Finally, the results of this analysis are briefly discussed.

  11. Dielectrophoretic manipulation of human chromosomes in microfluidic channels: extracting chromosome dielectric properties

    DEFF Research Database (Denmark)

    Clausen, Casper Hyttel; Dimaki, Maria; Buckley, Sonia;


    An investigation of the dielectric properties of polyamine buffer prepared human chromosomes is presented in this paper. Chromosomes prepared in this buffer are only a few micrometers in size and shaped roughly like spherical discs. Dielectrophoresis was therefore chosen as the method...... of manipulation combined with a custom designed microfluidic system containing the required electrodes for dielectrophoresis experiments. Our results show that although this system is presently not able to distinguish between the different chromosomes, it can provide average data for the dielectric properties...... of human chromosomes in polyamine buffer. These can then be used to optimize system designs for further characterization and even sorting. The experimental data from the dielectrophoretic manipulation were combined with theoretical calculations to extract a range of values for the permittivity...

  12. Sorting carbon nanotubes for electronics. (United States)

    Martel, Richard


    Because of their unique structure and composition, single-wall carbon nanotubes (SWNTs) are at the interface between molecules and crystalline solids. They also present properties that are ideal for making lightweight, inexpensive, and flexible electronics. The raw material is composed of a heterogeneous mixture of SWNTs that differ in helicity and diameter and, therefore, requires purification and separation. In a series of groundbreaking experiments, a robust process serving this purpose was developed based on SWNTs encapsulated in surfactants and water. Ultracentrifugation in a density gradient combined with surfactant mixtures provided buoyant density differences, enabling enrichment for both diameter and electronic properties. A new paper in this issue explores further the process through the hydrodynamic properties of SWNT-surfactant complexes. The study reveals that we have just begun to uncover the dynamics and properties of nanotube-surfactant interactions and highlights the potential that could be gained from a better understanding of their chemistry. The time scale of integration of carbon nanotubes into electronics applications remains unclear, but the recent developments in sorting out SWNTs paves the way for improving on the properties of network-based SWNTs.

  13. Enhancement of Selection, Bubble and Insertion Sorting Algorithm

    Directory of Open Access Journals (Sweden)

    Muhammad Farooq Umar


    Full Text Available In everyday life there is a large amount of data to arrange because sorting removes any ambiguities and make the data analysis and data processing very easy, efficient and provides with cost less effort. In this study a set of improved sorting algorithms are proposed which gives better performance and design idea. In this study five new sorting algorithms (Bi-directional Selection Sort, Bi-directional bubble sort, MIDBiDirectional Selection Sort, MIDBidirectional bubble sort and linear insertion sort are presented. Bi-directional Selection Sort and MIDBiDirectional Selection Sort are the enhancement on basic selection sort while Bidirectional bubble sort and MIDBidirectional bubble sort are the enhancement on basic bubble sort by changing the selection and swapping mechanism of data for sorting. Enhanced sorting algorithms reduced the iteration by half and quarter times respectively. Asymptotically complexities of these algorithms are reduced to O (n2/2 and O (n2/4 from O (n2. Linear insertion sort is the enhancement of insertion sort by changing the design of algorithm (convert two loops to one loop. So asymptotically this algorithm is converted to linear time complexity from quadratic complexity. These sorting algorithms are described using C. The proposed algorithms are analyzed using asymptotic analysis and also using machine-running time and compared with their basic sorting algorithms. In this study we also discuss how the performance and complexity can be improved by optimizing the code and design.

  14. Minimal Model Semantics for Sorted Constraint Representation

    Institute of Scientific and Technical Information of China (English)

    廖乐健; 史忠植


    Sorted constraint representation is a very useful representation in AI which combines class hierarchies and constraint networks.For such sorted constraint representation,a problem is how to generalize the idea of default inheritance to constraint network,where the attributes in a class or between different classes interact with each other via the network.To give a formal account for the defeasible reasoning in such representation,a general sorted constraint logic is proposed,and a minimal-model semantics for the logic is presented.

  15. An improved infrared technique for sorting pecans (United States)

    Graeve, Thorsten; Dereniak, Eustace L.; Lamonica, John A., Jr.


    This paper presents the results of a study of pecan spectral reflectances. It describes an experiment for measuring the contrast between several components of raw pecan product to be sorted. An analysis of the experimental data reveals high contrast ratios in the infrared spectrum, suggesting a potential improvement in sorting efficiency when separating pecan meat from shells. It is believed that this technique has the potential to dramatically improve the efficiency of current sorting machinery, and to reduce the cost of processing pecans for the consumer market.

  16. Visual ergonomics interventions in mail sorting facilities. (United States)

    Hemphälä, H; Hansson, G-Å; Dahlqvist, C; Eklund, J


    This study was performed between 2004 and 2011 at mail sorting facilities in Sweden. During this time, different interventions were performed. The first was a lighting intervention that had a positive impact on the postal workers, especially those with eyestrain. A new lighting system also improved the illuminance and gave better light distribution. The second intervention involved new personal spectacles for the postal workers who needed them and this had a positive effect on eyestrain. The third intervention involved a specific type of sorting spectacles for the postal workers who already used progressive lenses privately. The reading distances that the postal workers had while sorting the mail was inverted to the distances in their regular progressive lenses. The new sorting spectacles had a positive effect on head postures and on muscular activity.

  17. Quantum Database Search can do without Sorting

    CERN Document Server

    Patel, A


    Sorting is a fundamental computational process, which facilitates subsequent searching of a database. It can be thought of as factorisation of the search process. The location of a desired item in a sorted database can be found by classical queries that inspect one letter of the label at a time. For an unsorted database, no such classical quick search algorithm is available. If the database permits quantum queries, however, then mere digitisation is sufficient for efficient search. Sorting becomes redundant with the quantum superposition of states. A quantum algorithm is written down which locates the desired item in an unsorted database a factor of two faster than the best classical algorithm can in a sorted database. This algorithm has close resemblance to the assembly process in DNA replication.

  18. Sorting it out: regulation of exosome loading. (United States)

    Villarroya-Beltri, Carolina; Baixauli, Francesc; Gutiérrez-Vázquez, Cristina; Sánchez-Madrid, Francisco; Mittelbrunn, María


    Extracellular vesicles (EVs), a term that includes both exosomes of endocytic origin and vesicles derived from plasma membranes, are continuously secreted by cells to the extracellular environment, and represent a novel vehicle for cell-cell communication. Exosomes contain specific repertoires of proteins and RNAs, indicating the existence of mechanisms that control the sorting of molecules into them. Although the molecular mechanisms that regulate the loading of proteins into exosomes have been studied for years, the sorting of RNA has been elusive until recently. Here we review the molecular mechanisms that control the sorting of molecules into exosomes, with special attention to the sorting of RNA. We also discuss how the cellular context affects the composition of exosomes, and thus the outcome of the communication between the exosome-producer and recipient cells, with particular focus on the communication between tumor cells and with cells of the tumor microenvironment.

  19. Engineering a Cache-Oblivious Sorting Algorithm

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Vinther, Kristoffer


    This paper is an algorithmic engineering study of cache-oblivious sorting. We investigate by empirical methods a number of implementation issues and parameter choices for the cache-oblivious sorting algorithm Lazy Funnelsort, and compare the final algorithm with Quicksort, the established standard...... for comparison-based sorting, as well as with recent cache-aware proposals. The main result is a carefully implemented cache-oblivious sorting algorithm, which our experiments show can be faster than the best Quicksort implementation we are able to find, already for input sizes well within the limits of RAM....... It is also at least as fast as the recent cache-aware implementations included in the test. On disk the difference is even more pronounced regarding Quicksort and the cache-aware algorithms, whereas the algorithm is slower than a careful implementation of multiway Mergesort such as TPIE....

  20. Filter-less submicron hydrodynamic size sorting. (United States)

    Fouet, M; Mader, M-A; Iraïn, S; Yanha, Z; Naillon, A; Cargou, S; Gué, A-M; Joseph, P


    We propose a simple microfluidic device able to separate submicron particles (critical size ∼0.1 μm) from a complex sample with no filter (minimum channel dimension being 5 μm) by hydrodynamic filtration. A model taking into account the actual velocity profile and hydrodynamic resistances enables prediction of the chip sorting properties for any geometry. Two design families are studied to obtain (i) small sizes within minutes (low-aspect ratio, two-level chip) and (ii) micron-sized sorting with a μL flow rate (3D architecture based on lamination). We obtain quantitative agreement of sorting performances both with experiments and with numerical solving, and determine the limits of the approach. We therefore demonstrate a passive, filter-less sub-micron size sorting with a simple, robust, and easy to fabricate design.

  1. Isolation and characterization of DNA probes for human chromosome 21. (United States)

    Watkins, P C


    A coordinated effort to map and sequence the human genome has recently become a national priority. Chromosome 21, the smallest human chromosome accounting for less than 2% of the human genome, is an attractive model system for developing and evaluating genome mapping technology. Several strategies are currently being explored including the development of chromosome 21 libraries from somatic cell hybrids as reported here, the cloning of chromosome 21 in yeast artificial chromosomes (McCormick et al., 1989b), and the construction of chromosome 21 libraries using chromosome flow-sorting techniques (Fuscoe et al., 1989). This report describes the approaches used to identify DNA probes that are useful for mapping chromosome 21. Probes were successfully isolated from both phage and cosmid libraries made from two somatic cell hybrids that contain human chromosome 21 as the only human chromosome. The 15 cosmid clones from the WA17 library, reduced to cloned DNA sequences of an average size of 3 kb, total 525 kb of DNA which is approximately 1% of chromosome 21. From these clones, a set of polymorphic DNA markers that span the length of the long arm of chromosome 21 has been generated. All of the probes thus far analyzed from the WA17 libraries have been mapped to chromosome 21 both by physical and genetic mapping methods. It is therefore likely that the WA17 hybrid cell line contains human chromosome 21 as the only human component, in agreement with cytogenetic observation. The 153E7b cosmid libraries will provide an alternative source of cloned chromosome 21 DNA. Library screening techniques can be employed to obtain cloned DNA sequences from the same genetic loci of the two different chromosome 21s. Comparative analysis will allow direct estimation of DNA sequence variation for different regions of chromosome 21. Mapped DNA probes make possible the molecular analysis of chromosome 21 at a level of resolution not achievable by classical cytogenetic techniques (Graw et al

  2. Another Definition of Order—Sorted Algebra

    Institute of Scientific and Technical Information of China (English)



    In this paper the definition of order-sorted algebra is generalized by introducing transformation functions between subtypes and supertypes.According to our definition,a type needn't be a subset of its supertype and a record model may form an order-sorted algebra.A new definition of equation is given.It has also been proved that equational theories and describing single inheritance have the initial model.

  3. Automatic spike sorting using tuning information. (United States)

    Ventura, Valérie


    Current spike sorting methods focus on clustering neurons' characteristic spike waveforms. The resulting spike-sorted data are typically used to estimate how covariates of interest modulate the firing rates of neurons. However, when these covariates do modulate the firing rates, they provide information about spikes' identities, which thus far have been ignored for the purpose of spike sorting. This letter describes a novel approach to spike sorting, which incorporates both waveform information and tuning information obtained from the modulation of firing rates. Because it efficiently uses all the available information, this spike sorter yields lower spike misclassification rates than traditional automatic spike sorters. This theoretical result is verified empirically on several examples. The proposed method does not require additional assumptions; only its implementation is different. It essentially consists of performing spike sorting and tuning estimation simultaneously rather than sequentially, as is currently done. We used an expectation-maximization maximum likelihood algorithm to implement the new spike sorter. We present the general form of this algorithm and provide a detailed implementable version under the assumptions that neurons are independent and spike according to Poisson processes. Finally, we uncover a systematic flaw of spike sorting based on waveform information only.

  4. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.


    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  5. Laser ablation cell sorting in scanning cytometry (United States)

    Shen, Feimo; Price, Jeffrey H.


    Flow cytometry has been an important tool for automated cells sorting. However, the lack of good sensitivity prevents it from being used for rare events sorting; furthermore, fragile cells, anchorage-dependent cells, and clump forming cells cannot be sorted this way. A fully automated, high-speed scanning cytometer with autofocus and image segmentation is capable of accurately locating contaminant cells in a monolayer cell population. A laser ablation system was incorporated into the cytometer to negatively sort out the unwanted cells by applying a focused, ultra-short laser pulse (sub-micron diameter, pulse duration = 4 nsec, wavelength - 500 nm) to each targeted cell. Due to the high power density (approximately 1010 W/cm2) that was present at the focal point, disruptive mechanical forces were generated and were responsible for the kill. Fluorescently stained NIH-3T3 fibroblast cells were used as a model contaminant target ells in an unstained NIH-3T3 population to determine the identification-kill effectiveness. The contaminant cells were stained with the fluorochrome CellTracker Blue CMAC, whereas the background cells were left intact. Ablation pulses were applied in frame-by-frame increment batches to the cell culture on the microscope. The negative sorting effectiveness was analyzed by automatically re-scanning the post-ablation cell culture in phase contrast and propidium iodide stained epi fluorescent fields to verify cell death.

  6. Undetected sex chromosome aneuploidy by chromosomal microarray. (United States)

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay


    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  7. Applications of cell sorting in biotechnology

    Directory of Open Access Journals (Sweden)

    Mattanovich Diethard


    Full Text Available Abstract Due to its unique capability to analyze a large number of single cells for several parameters simultaneously, flow cytometry has changed our understanding of the behavior of cells in culture and of the population dynamics even of clonal populations. The potential of this method for biotechnological research, which is based on populations of living cells, was soon appreciated. Sorting applications, however, are still less frequent than one would expect with regard to their potential. This review highlights important contributions where flow cytometric cell sorting was used for physiological research, protein engineering, cell engineering, specifically emphasizing selection of overproducing cell lines. Finally conclusions are drawn concerning the impact of cell sorting on inverse metabolic engineering and systems biology.

  8. Order-Sorted Parameterization and Induction (United States)

    Meseguer, José

    Parameterization is one of the most powerful features to make specifications and declarative programs modular and reusable, and our best hope for scaling up formal verification efforts. This paper studies order-sorted parameterization at three different levels: (i) its mathematical semantics; (ii) its operational semantics by term rewriting; and (iii) the inductive reasoning principles that can soundly be used to prove properties about such specifications. It shows that achieving the desired properties at each of these three levels is a considerably subtler matter than for many-sorted specifications, but that such properties can be attained under reasonable conditions.

  9. Optical cell sorting with multiple imaging modalities

    DEFF Research Database (Denmark)

    Banas, Andrew; Carrissemoux, Caro; Palima, Darwin


    techniques. Scattering forces from beams actuated via efficient phase-only efficient modulation has been adopted. This has lowered the required power for sorting cells to a tenth of our previous approach, and also makes the cell sorter safer for use in clinical settings. With the versatility of dynamically...... programmable phase spatial light modulators, a plurality of light shaping techniques, including hybrid approaches, can be utilized in cell sorting....... healthy cells. With the richness of visual information, a lot of microscopy techniques have been developed and have been crucial in biological studies. To utilize their complementary advantages we adopt both fluorescence and brightfield imaging in our optical cell sorter. Brightfield imaging has...

  10. Birth of domestic cat kittens of predetermined sex after transfer of embryos produced by in vitro fertilization of oocytes with flow-sorted sperm. (United States)

    Pope, C E; Crichton, E G; Gómez, M C; Dumas, C; Dresser, B L


    Our goals were to: (1) determine if domestic cat sperm could be sorted to high purity by flow cytometry after overnight shipment of cooled samples; (2) evaluate the efficiency with which sorted sperm could be used to generate cat embryos in vitro; and (3) determine if live kittens of predetermined sex could be produced after transfer of embryos derived by IVF using sorted sperm. Semen samples (n=5) from one male were extended in electrolyte-free solution and shipped overnight at 4 degrees C to the sorting facility. Samples were adjusted to 75x10(6)sperm/mL and stained with Hoechst 33342. After 1h at 34.5 degrees C, samples were adjusted to 50x10(6)sperm/mL with 4% egg yolk TALP+0.002% food dye and sorted by high-speed flow cytometry. Later resort analysis confirmed purities of 94% and 83% for X- and Y-chromosome bearing sperm, respectively. Sorted sperm were centrifuged, re-suspended in TEST yolk buffer and shipped overnight to the IVF laboratory. After IVF of in vivo matured oocytes with X-chromosome bearing sperm, cleavage frequency was 62% (54/87). After IVF of IVM oocytes with control, X- or Y-chromosome bearing sperm, the incidence of cleavage was 42% (48/115), 33% (40/120), and 35% (52/150), respectively, and blastocyst development was 53% (21/40), 50% (11/22), and 55% (23/42), respectively (P>0.05). On Day 2, 45 embryos produced by IVF of in vivo matured oocytes with X-chromosome bearing sperm were transferred to the oviduct of four Day 1 recipients, three of which subsequently delivered litters of one, four, and seven female kittens, respectively. In conclusion, we confirmed that sperm sorting technology can be applied to domestic cats and established that kittens of predetermined sex can be produced.

  11. Micro and nanofluidic structures for cell sorting and genomic analysis (United States)

    Morton, Keith J.

    Microfluidic systems promise rapid analysis of small samples in a compact and inexpensive format. But direct scaling of lab bench protocols on-chip is challenging because laminar flows in typical microfluidic devices are characterized by non-mixing streamlines. Common microfluidic mixers and sorters work by diffusion, limiting application to objects that diffuse slowly such as cells and DNA. Recently Huang developed a passive microfluidic element to continuously separate bio-particles deterministically. In Deterministic Lateral Displacement (DLD), objects are sorted by size as they transit an asymmetric array of microfabricated posts. This thesis further develops DLD arrays with applications in three broad new areas. First the arrays are used, not simply to sort particles, but to move streams of cells through functional flows for chemical treatment---such as on-chip immunofluorescent labeling of blood cells with washing, and on-chip E.coli cell lysis with simultaneous chromosome extraction. Secondly, modular tiling of the basic DLD element is used to construct complex particle handling modes that include beam steering for jets of cells and beads. Thirdly, nanostructured DLD arrays are built using Nanoimprint Lithography (NIL) and continuous-flow separation of 100 nm and 200 nm size particles is demonstrated. Finally a number of ancillary nanofabrication techniques were developed in support of these overall goals, including methods to interface nanofluidic structures with standard microfluidic components such as inlet channels and reservoirs, precision etching of ultra-high aspect ratio (>50:1) silicon nanostructures, and fabrication of narrow (˜ 35 nm) channels used to stretch genomic length DNA.

  12. Chromosome painting reveals asynaptic full alignment of homologs and HIM-8-dependent remodeling of X chromosome territories during Caenorhabditis elegans meiosis.

    Directory of Open Access Journals (Sweden)

    Kentaro Nabeshima


    Full Text Available During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs with mobile patches of the nuclear envelope (NE-spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners.

  13. Integration through a Card-Sort Activity (United States)

    Green, Kris; Ricca, Bernard P.


    Learning to compute integrals via the various techniques of integration (e.g., integration by parts, partial fractions, etc.) is difficult for many students. Here, we look at how students in a college level Calculus II course develop the ability to categorize integrals and the difficulties they encounter using a card sort-resort activity. Analysis…

  14. Credit Scores, Race, and Residential Sorting (United States)

    Nelson, Ashlyn Aiko


    Credit scores have a profound impact on home purchasing power and mortgage pricing, yet little is known about how credit scores influence households' residential location decisions. This study estimates the effects of credit scores on residential sorting behavior using a novel mortgage industry data set combining household demographic, credit, and…

  15. Matlab Code for Sorted Real Schur Forms

    NARCIS (Netherlands)

    Brandts, J.H.


    In Matlab, there exists a standard command to generate a real Schur form, and another command transforms a real Schur form into a complex one. In Golub and Van Loan (1996), a Matlab-like routine is sketched that sorts a complex Schur form: given a target value ? in the complex plane, the diagonal el

  16. Sorting cells by their dynamical properties (United States)

    Henry, Ewan; Holm, Stefan H.; Zhang, Zunmin; Beech, Jason P.; Tegenfeldt, Jonas O.; Fedosov, Dmitry A.; Gompper, Gerhard


    Recent advances in cell sorting aim at the development of novel methods that are sensitive to various mechanical properties of cells. Microfluidic technologies have a great potential for cell sorting; however, the design of many micro-devices is based on theories developed for rigid spherical particles with size as a separation parameter. Clearly, most bioparticles are non-spherical and deformable and therefore exhibit a much more intricate behavior in fluid flow than rigid spheres. Here, we demonstrate the use of cells’ mechanical and dynamical properties as biomarkers for separation by employing a combination of mesoscale hydrodynamic simulations and microfluidic experiments. The dynamic behavior of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated for different device geometries and viscosity contrasts between the intra-cellular fluid and suspending medium. We find that the viscosity contrast and associated cell dynamics clearly determine the RBC trajectory through a DLD device. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices. Finally, we discuss the implications of cell dynamics for sorting schemes based on properties other than cell size, such as mechanics and morphology.

  17. Chromosome Disorder Outreach (United States)

    ... BLOG Join Us Donate You are not alone. Chromosome Disorder Outreach, Inc. is a non-profit organization, ... Support For all those diagnosed with any rare chromosome disorder. Since 1992, CDO has supported the parents ...

  18. Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). I. The genome homology of tundra vole, field vole, mouse and golden hamster revealed by comparative chromosome painting. (United States)

    Sitnikova, Natalia A; Romanenko, Svetlana A; O'Brien, Patricia C M; Perelman, Polina L; Fu, Beiyuan; Rubtsova, Nadezhda V; Serdukova, Natalya A; Golenishchev, Feodor N; Trifonov, Vladimir A; Ferguson-Smith, Malcolm A; Yang, Fengtang; Graphodatsky, Alexander S


    Cross-species chromosome painting has become the mainstay of comparative cytogenetic and chromosome evolution studies. Here we have made a set of chromosomal painting probes for the field vole (Microtus agrestis) by DOP-PCR amplification of flow-sorted chromosomes. Together with painting probes of golden hamster (Mesocricetus auratus) and mouse (Mus musculus), the field vole probes have been hybridized onto the metaphases of the tundra vole (Microtus oeconomus). A comparative chromosome map between these two voles, golden hamster and mouse has been established based on the results of cross-species chromosome painting and G-banding comparisons. The sets of paints from the field vole, golden hamster and mouse identified a total of 27, 40 and 47 homologous autosomal regions, respectively, in the genome of tundra vole; 16, 41 and 51 fusion/fission rearrangements differentiate the karyotype of the tundra vole from the karyotypes of the field vole, golden hamster and mouse, respectively.

  19. HURP permits MTOC sorting for robust meiotic spindle bipolarity, similar to extra centrosome clustering in cancer cells. (United States)

    Breuer, Manuel; Kolano, Agnieszka; Kwon, Mijung; Li, Chao-Chin; Tsai, Ting-Fen; Pellman, David; Brunet, Stéphane; Verlhac, Marie-Hélène


    In contrast to somatic cells, formation of acentriolar meiotic spindles relies on the organization of microtubules (MTs) and MT-organizing centers (MTOCs) into a stable bipolar structure. The underlying mechanisms are still unknown. We show that this process is impaired in hepatoma up-regulated protein (Hurp) knockout mice, which are viable but female sterile, showing defective oocyte divisions. HURP accumulates on interpolar MTs in the vicinity of chromosomes via Kinesin-5 activity. By promoting MT stability in the spindle central domain, HURP allows efficient MTOC sorting into distinct poles, providing bipolarity establishment and maintenance. Our results support a new model for meiotic spindle assembly in which HURP ensures assembly of a central MT array, which serves as a scaffold for the genesis of a robust bipolar structure supporting efficient chromosome congression. Furthermore, HURP is also required for the clustering of extra centrosomes before division, arguing for a shared molecular requirement of MTOC sorting in mammalian meiosis and cancer cell division.

  20. Chromosome painting in plants.

    NARCIS (Netherlands)

    Schubert, I.; Fransz, P.F.; Fuchs, J.; Jong, de J.H.


    The current 'state-of-art' as to chromosome painting in plants is reviewed. We define different situations described as painting so far: i) Genomic in situ hybridisation (GISH) with total genomic DNA to distinguish alien chromosomes on the basis of divergent dispersed repeats, ii) 'Chromosomal in si


    NARCIS (Netherlands)



    Banding techniques were carried out on metaphase chromosomes of zebrafish (Danio rerio) embryos. The karyotypes with the longest chromosomes consist of 12 metacentrics, 26 submetacentrics, and 12 subtelocentrics (2n = 50). All centromeres are C-band positive. Eight chromosomes have a pericentric C-b

  2. Development of a Prototype Automated Sorting System for Plastic Recycling

    Directory of Open Access Journals (Sweden)

    D. A. Wahab


    Full Text Available Automated sorting for plastic recyclables has been seen as the way forward in the plastic recycling industry. Automated sorting provides significant improvements in terms of efficiency and consistency in the sorting process. In the case of macro sorting, which is the most common type of automated sorting, efficiency is determined by the mechanical details of the material handling system as well as the detection system. This paper provides a review on the state of-the-art technologies that have been deployed by some of the recycling facilities abroad. The design and development of a cost effective prototype automated system for sorting plastic recyclables is proposed and discussed.

  3. Machine-vision based optofluidic cell sorting

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Bañas, Andrew

    In contemporary life science there is an increasing emphasis on sorting rare disease-indicating cells within small dilute quantities such as in the confines of optofluidic lab-on-chip devices. Our approach to this is based on the use of optical forces to isolate red blood cells detected by advanced...... machine vision1. This approach is gentler, less invasive and more economical compared to conventional FACS-systems. As cells are less responsive to plastic or glass objects commonly used in the optical manipulation literature2, and since laser safety would be an issue in clinical use, we develop efficient...... the available light and creating 2D or 3D beam distributions aimed at the positions of the detected cells. Furthermore, the beam shaping freedom provided by GPC can allow optimizations in the beam’s propagation and its interaction with the laser catapulted and sorted cells....

  4. Microtechnology for cell manipulation and sorting

    CERN Document Server

    Tseng, Peter; Carlo, Dino


    This book delves into the recent developments in the microscale and microfluidic technologies that allow manipulation at the single and cell aggregate level. Expert authors review the dominant mechanisms that manipulate and sort biological structures, making this a state-of-the-art overview of conventional cell sorting techniques, the principles of microfluidics, and of microfluidic devices. All chapters highlight the benefits and drawbacks of each technique they discuss, which include magnetic, electrical, optical, acoustic, gravity/sedimentation, inertial, deformability, and aqueous two-phase systems as the dominant mechanisms utilized by microfluidic devices to handle biological samples. Each chapter explains the physics of the mechanism at work, and reviews common geometries and devices to help readers decide the type of style of device required for various applications. This book is appropriate for graduate-level biomedical engineering and analytical chemistry students, as well as engineers and scientist...

  5. System for optical sorting of microscopic objects

    DEFF Research Database (Denmark)


    in a first reservoir, the one or more force units being suitable for optical momentum transfer. An electromagnetic radiation source (42) yields a radiation beam (31, 32) capable of optically displacing the force transfer units from one position to another within the first reservoir (1R). The force transfer...... units are displaced from positions away from the first objects to positions close to the first objects, and then displacing the first objects via a contact force (300) between the first objects and the force transfer units facilitates an optical sorting of the first objects and the second objects.......The present invention relates to a system for optical sorting of microscopic objects and corresponding method. An optical detection system (52) is capable of determining the positions of said first and/or said second objects. One or more force transfer units (200, 205, 210, 215) are placed...

  6. A mower detector to judge soil sorting

    Energy Technology Data Exchange (ETDEWEB)

    Bramlitt, E.T.; Johnson, N.R. [Thermo Nuclear Services, Inc., Albuquerque, NM (United States)


    Thermo Nuclear Services (TNS) has developed a mower detector as an inexpensive and fast means for deciding potential value of soil sorting for cleanup. It is a shielded detector box on wheels pushed over the ground (as a person mows grass) at 30 ft/min with gamma-ray counts recorded every 0.25 sec. It mirror images detection by the TNS transportable sorter system which conveys soil at 30 ft/min and toggles a gate to send soil on separate paths based on counts. The mower detector shows if contamination is variable and suitable for sorting, and by unique calibration sources, it indicates detection sensitivity. The mower detector has been used to characterize some soil at Department of Energy sites in New Jersey and South Carolina.

  7. Efficient sorting using registers and caches

    DEFF Research Database (Denmark)

    Wickremesinghe, Rajiv; Arge, Lars Allan; Chase, Jeffrey S.;


    Modern computer systems have increasingly complex memory systems. Common machine models for algorithm analysis do not reflect many of the features of these systems, e.g., large register sets, lockup-free caches, cache hierarchies, associativity, cache line fetching, and streaming behavior...... on sorting performance. We introduce a new cache-conscious sorting algorithm, R-MERGE, which achieves better performance in practice over algorithms that are superior in the theoretical models. R-MERGE is designed to minimize memory stall cycles rather than cache misses by considering features common to many....... Inadequate models lead to poor algorithmic choices and an incomplete understanding of algorithm behavior on real machines.A key step toward developing better models is to quantify the performance effects of features not reflected in the models. This paper explores the effect of memory system features...

  8. Sorting Network for Reversible Logic Synthesis

    CERN Document Server

    Islam, Md Saiful; Mahmud, Abdullah Al; karim, Muhammad Rezaul


    In this paper, we have introduced an algorithm to implement a sorting network for reversible logic synthesis based on swapping bit strings. The algorithm first constructs a network in terms of n*n Toffoli gates read from left to right. The number of gates in the circuit produced by our algorithm is then reduced by template matching and removing useless gates from the network. We have also compared the efficiency of the proposed method with the existing ones.

  9. Evaluating Effects of Cell Sorting on Cellular Integrity



    During the past year the Flow Cytometry Research Group has continued on its goal to establish best practice guidelines for cell sorting conditions that minimize cell stress, perturbation, or injury to the sorted cells. Towards this goal the group has followed up on an observation from our initial study that showed poor cell recovery when a clonal population of cells (Jurkat) was sorted aggressively under intentionally adverse sorting conditions (excessive pressure as well as undersized sortin...

  10. How Schwann Cells Sort Axons: New Concepts. (United States)

    Feltri, M Laura; Poitelon, Yannick; Previtali, Stefano Carlo


    Peripheral nerves contain large myelinated and small unmyelinated (Remak) fibers that perform different functions. The choice to myelinate or not is dictated to Schwann cells by the axon itself, based on the amount of neuregulin I-type III exposed on its membrane. Peripheral axons are more important in determining the final myelination fate than central axons, and the implications for this difference in Schwann cells and oligodendrocytes are discussed. Interestingly, this choice is reversible during pathology, accounting for the remarkable plasticity of Schwann cells, and contributing to the regenerative potential of the peripheral nervous system. Radial sorting is the process by which Schwann cells choose larger axons to myelinate during development. This crucial morphogenetic step is a prerequisite for myelination and for differentiation of Remak fibers, and is arrested in human diseases due to mutations in genes coding for extracellular matrix and linkage molecules. In this review we will summarize progresses made in the last years by a flurry of reverse genetic experiments in mice and fish. This work revealed novel molecules that control radial sorting, and contributed unexpected ideas to our understanding of the cellular and molecular mechanisms that control radial sorting of axons.

  11. Generalized sorting profile of alluvial fans (United States)

    Miller, Kimberly Litwin; Reitz, Meredith D.; Jerolmack, Douglas J.


    Alluvial rivers often exhibit self-similar gravel size distributions and abrupt gravel-sand transitions. Experiments suggest that these sorting patterns are established rapidly, but how—and how fast—this convergence occurs in the field is unknown. We examine the establishment of downstream sorting patterns in a kilometer-scale alluvial fan. The sharp transition from canyon to unconfined, channelized fan provides a well-defined boundary condition. The channel changes from deep and entrenched at the fan apex to shallow and depositional over a short distance, exhibiting nonequilibrium behavior. The resulting gravel-fining profile is not self-similar; the particle size distribution narrows until approximate equal mobility is achieved. Downfan, the gravel-sand transition appears to exhibit a self-similar form; field and laboratory data collapse when downstream distance is normalized by the location of the transition. Results suggest a generalized sorting profile for alluvial fans as a consequence of the threshold of motion and nonequilibrium channels.

  12. Categorizing Variations of Student-Implemented Sorting Algorithms (United States)

    Taherkhani, Ahmad; Korhonen, Ari; Malmi, Lauri


    In this study, we examined freshmen students' sorting algorithm implementations in data structures and algorithms' course in two phases: at the beginning of the course before the students received any instruction on sorting algorithms, and after taking a lecture on sorting algorithms. The analysis revealed that many students have insufficient…

  13. Gender Sorting across K-12 Schools in the United States (United States)

    Long, Mark C.; Conger, Dylan


    This article documents evidence of nonrandom gender sorting across K-12 schools in the United States. The sorting exists among coed schools and at all grade levels, and it is highest in the secondary school grades. We observe some gender sorting across school sectors and types: for instance, males are slightly underrepresented in private schools…

  14. Chromosomal instability in meningiomas. (United States)

    van Tilborg, Angela A G; Al Allak, Bushra; Velthuizen, Sandra C J M; de Vries, Annie; Kros, Johan M; Avezaat, Cees J J; de Klein, Annelies; Beverloo, H Berna; Zwarthoff, Ellen C


    Approximately 60% of sporadic meningiomas are caused by inactivation of the NF2 tumor suppressor gene on chromosome 22. No causative gene is known for the remaining 40%. Cytogenetic analysis shows that meningiomas caused by inactivation of the NF2 gene can be divided into tumors that show monosomy 22 as the sole abnormality and tumors with a more complex karyotype. Meningiomas not caused by the NF2 gene usually have a diploid karyotype. Here we report that, besides the clonal chromosomal aberrations, the chromosome numbers in many meningiomas varied from one metaphase spread to the other, a feature that is indicative of chromosomal instability. Unexpectedly and regardless of genotype, a subgroup of tumors was observed with an average number of 44.9 chromosomes and little variation in the number of chromosomes per metaphase spread. In addition, a second subgroup was recognized with a hyperdiploid number of chromosomes (average 48.5) and considerable variation in numbers per metaphase. However, this numerical instability resulted in a clonal karyotype with chromosomal gains and losses in addition to loss of chromosome 22 only in meningiomas caused by inactivation of the NF2 gene. In cultured cells of all tumor groups, bi- and multinucleated cells were seen, as well as anaphase bridges, residual chromatid strings, multiple spindle poles, and unseparated chromatids, suggesting defects in the mitotic apparatus or kinetochore. Thus, we conclude that even a benign and slow-growing tumor like a meningioma displays chromosomal instability.

  15. HLA-targeted flow cytometric sorting of blood cells allows separation of pure and viable microchimeric cell populations. (United States)

    Drabbels, Jos J M; van de Keur, Carin; Kemps, Berit M; Mulder, Arend; Scherjon, Sicco A; Claas, Frans H J; Eikmans, Michael


    Microchimerism is defined by the presence of low levels of nonhost cells in a person. We developed a reliable method for separating viable microchimeric cells from the host environment. For flow cytometric cell sorting, HLA antigens were targeted with human monoclonal HLA antibodies (mAbs). Optimal separation of microchimeric cells (present at a proportion as low as 0.01% in artificial mixtures) was obtained with 2 different HLA mAbs, one targeting the chimeric cells and the other the background cells. To verify purity of separated cell populations, flow-sorted fractions of 1000 cells were processed for DNA analysis by HLA-allele-specific and Y-chromosome-directed real-time quantitative PCR assays. After sorting, PCR signals of chimeric DNA markers in the positive fractions were significantly enhanced compared with those in the presort samples, and they were similar to those in 100% chimeric control samples. Next, we demonstrate applicability of HLA-targeted FACS sorting after pregnancy by separating chimeric maternal cells from child umbilical cord mononuclear cells. Targeting allelic differences with anti-HLA mAbs with FACS sorting allows maximal enrichment of viable microchimeric cells from a background cell population. The current methodology enables reliable microchimeric cell detection and separation in clinical specimens.

  16. Analysis of plant meiotic chromosomes by chromosome painting. (United States)

    Lysak, Martin A; Mandáková, Terezie


    Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome arms, or entire chromosomes via fluorescence in situ hybridization (FISH). For CP in plants, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the target species or from a closely related species (comparative chromosome painting, CCP) are typically applied as painting probes. Extended pachytene chromosomes provide the highest resolution of CP in plants. CP enables identification and tracing of particular chromosome regions and/or entire chromosomes throughout all meiotic stages as well as corresponding chromosome territories in premeiotic interphase nuclei. Meiotic pairing and structural chromosome rearrangements (typically inversions and translocations) can be identified by CP. Here, we describe step-by-step protocols of CP and CCP in plant species including chromosome preparation, BAC DNA labeling, and multicolor FISH.

  17. Cache-Aware and Cache-Oblivious Adaptive Sorting

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Moruz, Gabriel


    Two new adaptive sorting algorithms are introduced which perform an optimal number of comparisons with respect to the number of inversions in the input. The first algorithm is based on a new linear time reduction to (non-adaptive) sorting. The second algorithm is based on a new division protocol ...... for the GenericSort algorithm by Estivill-Castro and Wood. From both algorithms we derive I/O-optimal cache-aware and cache-oblivious adaptive sorting algorithms. These are the first I/O-optimal adaptive sorting algorithms....

  18. The Precarious Prokaryotic Chromosome


    Kuzminov, Andrei


    Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the t...

  19. Mechanisms for chromosome segregation. (United States)

    Bouet, Jean-Yves; Stouf, Mathieu; Lebailly, Elise; Cornet, François


    Bacteria face the problem of segregating their gigantic chromosomes without a segregation period restricted in time and space, as Eukaryotes do. Segregation thus involves multiple activities, general or specific of a chromosome region and differentially controlled. Recent advances show that these various mechanisms conform to a “pair and release” rule, which appears as a general rule in DNA segregation. We describe the latest advances in segregation of bacterial chromosomes with emphasis on the different pair and release mechanisms.

  20. Bacterial chromosome segregation. (United States)

    Possoz, Christophe; Junier, Ivan; Espeli, Olivier


    Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with model organisms: Escherichia coli, Bacillus subtilis, Caulobacter crescentus and Vibrio cholerae. We describe the global positionning of the nucleoid in the cell and the specific localization and dynamics of different chromosomal loci, kinetic and biophysic aspects of chromosome segregation are presented. Finally, a presentation of the key proteins involved in the chromosome segregation is made.

  1. Chromosome oscillations in mitosis (United States)

    Campas, Otger


    Successful cell division necessitates a tight regulation of chromosome movement via the activity of molecular motors. Many of the key players at the origin of the forces generating the motion have been identified, but their spatial and temporal organization remains elusive. In animal cells, chromosomes periodically switch between phases of movement towards and away from the pole. This characteristic oscillatory behaviour cannot be explained by the current models of chromosome positioning and congression. We perform a self-contained theoretical analysis in which the motion of mono-oriented chromosomes results from the competition between the activity of the kinetochore and chromokinesin motors on the chromosome arms. Our analysis, consistent with the available experimental data, proposes that the interplay between the aster-like morphology of the spindle and the collective kinetics of molecular motors is at the origin of chromosome oscillations, positioning and congression. It provides a natural explanation for the so-called chromosome directional instability and for the mechanism by which chromosomes sense their position in space. In addition, we estimate the in vivo velocity of chromokinesins at vanishing load and propose new experiments to assess the mechanism at the origin of chromosome movement in cell division.

  2. Stochastic Models of Vesicular Sorting in Cellular Organelles

    CERN Document Server

    Vagne, Quentin


    The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...

  3. Fetal chromosome analysis: screening for chromosome disease?

    DEFF Research Database (Denmark)

    Philip, J; Tabor, Ann; Bang, J


    The aim of the study was to investigate the rationale of the current indications for fetal chromosome analysis. 5372 women had 5423 amniocentesis performed, this group constituting a consecutive sample at the chromosome laboratory, Rigshospitalet, Copenhagen from March 1973 to September 1980 (Group...... to women having amniocentesis, although considered not to have any increased risk of fetal chromosome abnormality (1390 pregnancies, group B). They were also compared with 750 consecutive pregnancies in women 25-34 years of age, in whom all heritable diseases were excluded (group C). The risk of unbalanced...... with women without elevated risk. Spontaneous abortion rate and prematurity rate did not differ from rates expected without amniocentesis. It is concluded that current indications may be characterized as a mixture of evident high risk factors and factors with only a minor influence on risk. Indications...

  4. Sorting waste - A question of good will

    CERN Multimedia

    TS Department - FM Group


    In order to minimise waste-sorting costs, CERN provides two types of container at the entrance of buildings: a green plastic container for paper/cardboard and a metal container for household-type waste. We regret that recently there has been a significant decrease in the extent to which these types of waste are sorted, for example green containers have been found to hold assorted waste such as cardboard boxes filled with polystyrene, bubble-wrap or even plastic bottles, yoghurt pots, etc. Checks have shown that this 'non-compliant' waste does not come from the rubbish bins emptied by the cleaners but is deposited there directly by inconsiderate users. During the months of October and November alone, for example, only 15% of the waste from the paper/cardboard containers was recycled and the remaining 85% had to be incinerated, which entails a high cost for CERN. You should note that once an item of non-compliant waste is found in a green container its contents are immediately sent as waste to be incinerated ...

  5. Human-powered Sorts and Joins

    CERN Document Server

    Marcus, Adam; Karger, David; Madden, Samuel; Miller, Robert


    Crowdsourcing markets like Amazon's Mechanical Turk (MTurk) make it possible to task people with small jobs, such as labeling images or looking up phone numbers, via a programmatic interface. MTurk tasks for processing datasets with humans are currently designed with significant reimplementation of common workflows and ad-hoc selection of parameters such as price to pay per task. We describe how we have integrated crowds into a declarative workflow engine called Qurk to reduce the burden on workflow designers. In this paper, we focus on how to use humans to compare items for sorting and joining data, two of the most common operations in DBMSs. We describe our basic query interface and the user interface of the tasks we post to MTurk. We also propose a number of optimizations, including task batching, replacing pairwise comparisons with numerical ratings, and pre-filtering tables before joining them, which dramatically reduce the overall cost of running sorts and joins on the crowd. In an experiment joining tw...

  6. Quantum bounds for ordered searching and sorting

    CERN Document Server

    Hoyer, P; Shi, Y; Hoyer, Peter; Neerbek, Jan; Shi, Yaoyun


    We consider the quantum complexities of searching an ordered list and sorting an un-ordered list. For searching an ordered list of N elements, we prove a lower bound of \\frac{1}{\\pi}(\\ln(N)-1) on the number of oracle queries that access the list elements. This improves the previously best lower bound of ({1/12}\\log_2(N) - O(1)) due to Ambainis. For sorting N numbers, we prove a lower bound of \\frac{N}{2\\pi}(\\ln(N)-1) on the number of binary comparisons. The previously best lower bound is \\Omega(N). Our proofs are based on a weighted all-pairs inner product argument, and our results generalize to bounded error quantum algorithms. Both results are proven in the so-called quantum black box model, a quantum analogue of classical decision trees. In addition to our lower bound results, we give an exact quantum algorithm for ordered searching using (\\log_3(N) + O(1)) queries, which is roughly 0.631 \\log_2(N). Although our algorithm is worse than that of Farhi, Goldstone, Gutmann and Sipser, which makes 0.526 \\log_2(...

  7. Corner Sort for Pareto-Based Many-Objective Optimization. (United States)

    Wang, Handing; Yao, Xin


    Nondominated sorting plays an important role in Pareto-based multiobjective evolutionary algorithms (MOEAs). When faced with many-objective optimization problems multiobjective optimization problems (MOPs) with more than three objectives, the number of comparisons needed in nondominated sorting becomes very large. In view of this, a new corner sort is proposed in this paper. Corner sort first adopts a fast and simple method to obtain a nondominated solution from the corner solutions, and then uses the nondominated solution to ignore the solutions dominated by it to save comparisons. Obtaining the nondominated solutions requires much fewer objective comparisons in corner sort. In order to evaluate its performance, several state-of-the-art nondominated sorts are compared with our corner sort on three kinds of artificial solution sets of MOPs and the solution sets generated from MOEAs on benchmark problems. On one hand, the experiments on artificial solution sets show the performance on the solution sets with different distributions. On the other hand, the experiments on the solution sets generated from MOEAs show the influence that different sorts bring to MOEAs. The results show that corner sort performs well, especially on many-objective optimization problems. Corner sort uses fewer comparisons than others.

  8. XYY chromosome anomaly and schizophrenia. (United States)

    Rajagopalan, M; MacBeth, R; Varma, S L


    Sex chromosome anomalies have been associated with psychoses, and most of the evidence is linked to the presence of an additional X chromosome. We report a patient with XYY chromosome anomaly who developed schizophrenia.

  9. Vertical sorting and the morphodynamics of bed form-dominated rivers: a sorting evolution model

    NARCIS (Netherlands)

    Blom, Astrid; Ribberink, Jan S.; Parker, Gary


    Existing sediment continuity models for nonuniform sediment suffer from a number of shortcomings, as they fail to describe vertical sorting fluxes other than through net aggradation or degradation of the bed and are based on a discrete representation of the bed material interacting with the flow. We

  10. Chromosome homologies of the highly rearranged karyotypes of four Akodon species (Rodentia, Cricetidae) resolved by reciprocal chromosome painting: the evolution of the lowest diploid number in rodents. (United States)

    Ventura, Karen; O'Brien, Patricia C M; Yonenaga-Yassuda, Yatiyo; Ferguson-Smith, Malcolm A


    Traditionally comparative cytogenetic studies are based mainly on banding patterns. Nevertheless, when dealing with species with highly rearranged genomes, as in Akodon species, or with other highly divergent species, cytogenetic comparisons of banding patterns prove inadequate. Hence, comparative chromosome painting has become the method of choice for genome comparisons at the cytogenetic level since it allows complete chromosome probes of a species to be hybridized in situ onto chromosomes of other species, detecting homologous genomic regions between them. In the present study, we have explored the highly rearranged complements of the Akodon species using reciprocal chromosome painting through species-specific chromosome probes obtained by chromosome sorting. The results revealed complete homology among the complements of Akodon sp. n. (ASP), 2n = 10; Akodon cursor (ACU), 2n = 15; Akodon montensis (AMO), 2n = 24; and Akodon paranaensis (APA), 2n = 44, and extensive chromosome rearrangements have been detected within the species with high precision. Robertsonian and tandem rearrangements, pericentric inversions and/or centromere repositioning, paracentric inversion, translocations, insertions, and breakpoints, where chromosomal rearrangements, seen to be favorable, were observed. Chromosome painting using the APA set of 21 autosomes plus X and Y revealed eight syntenic segments that are shared with A. montensis, A. cursor, and ASP, and one syntenic segment shared by A. montensis and A. cursor plus five exclusive chromosome associations for A. cursor and six for ASP chromosome X, except for the heterochromatin region of ASP X, and even chromosome Y shared complete homology among the species. These data indicate that all those closely related species have experienced a recent extensive process of autosomal rearrangement in which, except for ASP, there is still complete conservation of sex chromosomes homologies.

  11. Fluorescence activated cell sorting of plant protoplasts. (United States)

    Bargmann, Bastiaan O R; Birnbaum, Kenneth D


    High-resolution, cell type-specific analysis of gene expression greatly enhances understanding of developmental regulation and responses to environmental stimuli in any multicellular organism. In situ hybridization and reporter gene visualization can to a limited extent be used to this end but for high resolution quantitative RT-PCR or high-throughput transcriptome-wide analysis the isolation of RNA from particular cell types is requisite. Cellular dissociation of tissue expressing a fluorescent protein marker in a specific cell type and subsequent Fluorescence Activated Cell Sorting (FACS) makes it possible to collect sufficient amounts of material for RNA extraction, cDNA synthesis/amplification and microarray analysis. An extensive set of cell type-specific fluorescent reporter lines is available to the plant research community. In this case, two marker lines of the Arabidopsis thaliana root are used: P(SCR;)::GFP (endodermis and quiescent center) and P(WOX5;)::GFP (quiescent center). Large numbers (thousands) of seedlings are grown hydroponically or on agar plates and harvested to obtain enough root material for further analysis. Cellular dissociation of plant material is achieved by enzymatic digestion of the cell wall. This procedure makes use of high osmolarity-induced plasmolysis and commercially available cellulases, pectinases and hemicellulases to release protoplasts into solution. FACS of GFP-positive cells makes use of the visualization of the green versus the red emission spectra of protoplasts excited by a 488 nm laser. GFP-positive protoplasts can be distinguished by their increased ratio of green to red emission. Protoplasts are typically sorted directly into RNA extraction buffer and stored for further processing at a later time. This technique is revealed to be straightforward and practicable. Furthermore, it is shown that it can be used without difficulty to isolate sufficient numbers of cells for transcriptome analysis, even for very scarce

  12. Sequential cloning of chromosomes (United States)

    Lacks, S.A.


    A method for sequential cloning of chromosomal DNA of a target organism is disclosed. A first DNA segment homologous to the chromosomal DNA to be sequentially cloned is isolated. The first segment has a first restriction enzyme site on either side. A first vector product is formed by ligating the homologous segment into a suitably designed vector. The first vector product is circularly integrated into the target organism`s chromosomal DNA. The resulting integrated chromosomal DNA segment includes the homologous DNA segment at either end of the integrated vector segment. The integrated chromosomal DNA is cleaved with a second restriction enzyme and ligated to form a vector-containing plasmid, which is replicated in a host organism. The replicated plasmid is then cleaved with the first restriction enzyme. Next, a DNA segment containing the vector and a segment of DNA homologous to a distal portion of the previously isolated DNA segment is isolated. This segment is then ligated to form a plasmid which is replicated within a suitable host. This plasmid is then circularly integrated into the target chromosomal DNA. The chromosomal DNA containing the circularly integrated vector is treated with a third, retrorestriction (class IIS) enzyme. The cleaved DNA is ligated to give a plasmid that is used to transform a host permissive for replication of its vector. The sequential cloning process continues by repeated cycles of circular integration and excision. The excision is carried out alternately with the second and third enzymes. 9 figs.

  13. Chromosomal mosaicism goes global

    Directory of Open Access Journals (Sweden)

    Yurov Yuri B


    Full Text Available Intercellular differences of chromosomal content in the same individual are defined as chromosomal mosaicism (alias intercellular or somatic genomic variations or, in a number of publications, mosaic aneuploidy. It has long been suggested that this phenomenon poorly contributes both to intercellular (interindividual diversity and to human disease. However, our views have recently become to change due to a series of communications demonstrated a higher incidence of chromosomal mosaicism in diseased individuals (major psychiatric disorders and autoimmune diseases as well as depicted chromosomal mosaicism contribution to genetic diversity, the central nervous system development, and aging. The later has been produced by significant achievements in the field of molecular cytogenetics. Recently, Molecular Cytogenetics has published an article by Maj Hulten and colleagues that has provided evidences for chromosomal mosaicism to underlie formation of germline aneuploidy in human female gametes using trisomy 21 (Down syndrome as a model. Since meiotic aneuploidy is suggested to be the leading genetic cause of human prenatal mortality and postnatal morbidity, these data together with previous findings define chromosomal mosaicism not as a casual finding during cytogenetic analyses but as a more significant biological phenomenon than previously recognized. Finally, the significance of chromosomal mosaicism can be drawn from the fact, that this phenomenon is involved in genetic diversity, normal and abnormal prenatal development, human diseases, aging, and meiotic aneuploidy, the intrinsic cause of which remains, as yet, unknown.

  14. Receptorligand sorting along the endocytic pathway

    CERN Document Server

    Linderman, Jennifer J


    This research monograph focuses on a biomolecular separation process that occurs within most cells. Two types of molecules, receptors and ligands, are separated and routed along different intracellular pathways; this is a critical step in the process of receptor-mediated endocytosis. The development of an understanding of the basic mechanisms of this separation process is presented, with an emphasis on discovering the fundamental and measurable parameters that influence the event. Mathematical models of sorting are evaluated to predict the range of possible outcomes. These are compared with a variety of experimental data on different receptor/ligand systems. In addition, the influence of the separation on overall receptor/ligand processing dynamics is discussed. The book is intended for both biomathematicians and biologists. It is not necessary to understand the details of the model equations and their solution in order to test the models experimentally. The analysis suggests experiments that might be done to...

  15. Cell sorting using efficient light shaping approaches

    DEFF Research Database (Denmark)


    and light modulation devices. The Generalized Phase Contrast (GPC) method that can be used for efficiently illuminating spatial light modulators or creating well-defined contiguous optical traps is supplemented by diffractive techniques capable of integrating the available light and creating 2D or 3D beam......Early detection of diseases can save lives. Hence, there is emphasis in sorting rare disease-indicating cells within small dilute quantities such as in the confines of lab-on-a-chip devices. In our work, we use optical forces to isolate red blood cells detected by machine vision. This approach...... is gentler, less invasive and more economical compared to conventional FACS systems. As cells are less responsive to plastic or glass beads commonly used in the optical manipulation literature, and since laser safety would be an issue in clinical use, we develop efficient approaches in utilizing lasers...

  16. Passive chip-based droplet sorting

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Lee, Abraham P; Hatch, Andrew C; Fisher, Jeffrey S


    An apparatus for passive sorting of microdroplets including a main flow channel, a flow stream of microdroplets in the main flow channel wherein the microdroplets have substantially the same diameter and wherein the flow stream of microdroplets includes first microdroplets having a first degree of stiffness and second microdroplets having a second degree of stiffness wherein the second degree of stiffness is different than the first degree of stiffness. A second flow channel is connected to the main flow channel for the second microdroplets having a second degree of stiffness. A separator separates the second microdroplets having a second degree of stiffness from the first microdroplets and directs the second microdroplets having a second degree of stiffness into the second flow channel.

  17. Passive chip-based droplet sorting

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Lee, Abraham P; Hatch, Andrew C; Fisher, Jeffrey S


    An apparatus for passive sorting of microdroplets including a main flow channel, a flow stream of microdroplets in the main flow channel wherein the microdroplets have substantially the same diameter and wherein the flow stream of microdroplets includes first microdroplets having a first degree of stiffness and second microdroplets having a second degree of stiffness wherein the second degree of stiffness is different than the first degree of stiffness. A second flow channel is connected to the main flow channel for the second microdroplets having a second degree of stiffness. A separator separates the second microdroplets having a second degree of stiffness from the first microdroplets and directs the second microdroplets having a second degree of stiffness into the second flow channel.

  18. Carbon Nanotube–Purification and Sorting Protocols

    Directory of Open Access Journals (Sweden)

    Poornendu Chaturvedi


    Full Text Available Carbon nanotubes (CNTs have shown extraordinary mechanical, thermal, electrical, and electronic properties. Electronic properties of CNT are very sensitive to its diameter and chirality, making it metallicor semiconducting, depending upon its chiral vector. The extraordinary properties of CNTs have led to demonstration of several applications but commercial realisation of these devices require consistent qualityof CNTs, and these should be  free of any impurity. For development of electronic devices, CNTs should notjust be pure but also of similar length, diameter, and electronic behaviour. Such demanding requirements need development of elaborate purification and sorting protocols. In this paper,  a brief review of the existing technologies and the research done is presented.Defence Science Journal, 2008, 58(5, pp.591-599, DOI:

  19. Learning sorting algorithms through visualization construction (United States)

    Cetin, Ibrahim; Andrews-Larson, Christine


    Recent increased interest in computational thinking poses an important question to researchers: What are the best ways to teach fundamental computing concepts to students? Visualization is suggested as one way of supporting student learning. This mixed-method study aimed to (i) examine the effect of instruction in which students constructed visualizations on students' programming achievement and students' attitudes toward computer programming, and (ii) explore how this kind of instruction supports students' learning according to their self-reported experiences in the course. The study was conducted with 58 pre-service teachers who were enrolled in their second programming class. They expect to teach information technology and computing-related courses at the primary and secondary levels. An embedded experimental model was utilized as a research design. Students in the experimental group were given instruction that required students to construct visualizations related to sorting, whereas students in the control group viewed pre-made visualizations. After the instructional intervention, eight students from each group were selected for semi-structured interviews. The results showed that the intervention based on visualization construction resulted in significantly better acquisition of sorting concepts. However, there was no significant difference between the groups with respect to students' attitudes toward computer programming. Qualitative data analysis indicated that students in the experimental group constructed necessary abstractions through their engagement in visualization construction activities. The authors of this study argue that the students' active engagement in the visualization construction activities explains only one side of students' success. The other side can be explained through the instructional approach, constructionism in this case, used to design instruction. The conclusions and implications of this study can be used by researchers and




    Studies of the chromosomes of four American marsupials demonstrated that Caluromys derbianus and Marmosa mexicana have a diploid number of 14 chromosomes, and that Philander opossum and Didelphis marsupialis have a diploid number of 22. The karyotypes of C. derbianus and M. mexicana are similar, whereas those of P. opossum and D. marsupialis are dissimilar. If the 14-chromosome karyotype represents a reduction from a primitive number of 22, these observations suggest that the change has occurred independently in the American and Australasian forms.

  1. Pattern matching based active optical sorting of colloids/cells (United States)

    Verma, R. S.; Dasgupta, R.; Ahlawat, S.; Kumar, N.; Uppal, A.; Gupta, P. K.


    We report active optical sorting of colloids/cells by employing a cross correlation based pattern matching technique for selection of the desired objects and thereafter sorting using dynamically controllable holographic optical traps. The problem of possible collision between the different sets of objects during sorting was avoided by raising one set of particles to a different plane. We also present the results obtained on using this approach for some representative applications such as sorting of silica particles of two different sizes, of closely packed colloids and of white blood cells and red blood cells from a mixture of the two.

  2. Improved method for pulse sorting based on PRI transform (United States)

    Ren, Chunhui; Cao, Junqing; Fu, Yusheng; Barner, Kenneth E.


    To solve the problem of pulse sorting in complex electromagnetic environment, we propose an improved method for pulse sorting through in-depth analysis of the PRI transform algorithm principle and the advantages and disadvantages in this paper. The method is based on the traditional PRI transform algorithm, using spectral analysis of PRI transform spectrum to estimate the PRI centre value of jitter signal. Simulation results indicate that, the improved sorting method overcome the shortcomings of the traditional PRI jitter separation algorithm which cannot effectively sort jitter pulse sequence, in addition to the advantages of simple and accurate.

  3. A many-sorted calculus based on resolution and paramodulation

    CERN Document Server

    Walther, Christoph


    A Many-Sorted Calculus Based on Resolution and Paramodulation emphasizes the utilization of advantages and concepts of many-sorted logic for resolution and paramodulation based automated theorem proving.This book considers some first-order calculus that defines how theorems from given hypotheses by pure syntactic reasoning are obtained, shifting all the semantic and implicit argumentation to the syntactic and explicit level of formal first-order reasoning. This text discusses the efficiency of many-sorted reasoning, formal preliminaries for the RP- and ?RP-calculus, and many-sorted term rewrit

  4. Chromosomal abnormalities and autism

    Directory of Open Access Journals (Sweden)

    Farida El-Baz


    Conclusion: Chromosomal abnormalities were not detected in the studied autistic children, and so the relation between the genetics and autism still needs further work up with different study methods and techniques.

  5. [Sex chromosomes and meiosis]. (United States)

    Guichaoua, M-R; Geoffroy-Siraudin, C; Tassistro, V; Ghalamoun-Slaimi, R; Perrin, J; Metzler-Guillemain, C


    Sex chromosome behaviour fundamentally differs between male and female meiosis. In oocyte, X chromosomes synapse giving a XX bivalent which is not recognizable in their morphology and behaviour from autosomal bivalents. In human male, X and Y chromosomes differ from one another in their morphology and their genetic content, leading to a limited pairing and preventing genetic recombination, excepted in homologous region PAR1. During pachytene stage of the first meiotic prophase, X and Y chromosomes undergo a progressive condensation and form a transcriptionally silenced peripheral XY body. The condensation of the XY bivalent during pachytene stage led us to describe four pachytene substages and to localize the pachytene checkpoint between substages 2 and 3. We also defined the pachytene index (PI=P1+P2/P1+P2+P3+P4) which is always less than 0.50 in normal meiosis. XY body undergoes decondensation at diplotene stage, but transcriptional inactivation of the two sex chromosomes or Meiotic Sex Chromosome Inactivation (MSCI) persists through to the end of spermatogenesis. Sex chromosome inactivation involves several proteins, some of them were now identified. Two isoforms of the HP1 protein, HP1beta and HP1gamma, are involved in the facultative heterochromatinization of the XY body, but the initiation of this process involves the phosphorylation of the protein H2AX by the kinase ATR whose recruitment depends on BRCA1. Extensive researches on the inactivation of the sex chromosomes during male meiosis will allow to a better understanding of some male infertilities.

  6. Chromosome doubling method (United States)

    Kato, Akio


    The invention provides methods for chromosome doubling in plants. The technique overcomes the low yields of doubled progeny associated with the use of prior techniques for doubling chromosomes in plants such as grasses. The technique can be used in large scale applications and has been demonstrated to be highly effective in maize. Following treatment in accordance with the invention, plants remain amenable to self fertilization, thereby allowing the efficient isolation of doubled progeny plants.

  7. Viable cell sorting of dinoflagellates by multiparametric flow cytometry. (United States)

    Sinigalliano, Christopher D; Winshell, Jamie; Guerrero, Maria A; Scorzetti, Gloria; Fell, Jack W; Eaton, Richard W; Brand, Larry; Rein, Kathleen S


    Electronic cell sorting for isolation and culture of dinoflagellates and other marine eukaryotic phytoplankton was compared to the traditional method of manually picking cells using a micropipette. Trauma to electronically sorted cells was not a limiting factor, as fragile dinoflagellates, such as Karenia brevis (Dinophyceae), survived electronic cell sorting to yield viable cells. The rate of successful isolation of large-scale (> 4 litres) cultures was higher for manual picking than for electronic cell sorting (2% vs 0.5%, respectively). However, manual picking of cells is more labor intensive and time consuming. Most manually isolated cells required repicking, as the cultures were determined not to be unialgal after a single round of isolation; whereas, no cultures obtained in this study from electronic single-cell sorting required resorting. A broad flow cytometric gating logic was employed to enhance species diversity. The percentages of unique genotypes produced by manual picking or electronic cell sorting were similar (57% vs 54%, respectively), and each approach produced a variety of dinoflagellate or raphidophyte genera. Alternatively, a highly restrictive gating logic was successfully used to target K. brevis from a natural bloom sample. Direct electronic single-cell sorting was more successful than utilizing a pre-enrichment sort followed by electronic single-cell sorting. The appropriate recovery medium may enhance the rate of successful isolations. Seventy percent of isolated cells were recovered in a new medium (RE) reported here, which was optimized for axenic dinoflagellate cultures. The greatest limiting factor to the throughput of electronic cell sorting is the need for manual postsort culture maintenance and assessment of the large number of isolated cells. However, when combined with newly developed automated methods for growth screening, electronic single-cell sorting has the potential to accelerate the discovery of new algal strains.

  8. Activation of X Chromosome Inactivation

    NARCIS (Netherlands)

    C.M. Maduro (Cheryl)


    markdownabstractIn mammals, males are the heterogametic sex having an X chromosome and a Y chromosome whereas females have two X chromosomes. Despite originating from an ancient homologous autosomal pair, the X and Y chromosome now differ greatly in size and gene content after ~180 MY of evolution.

  9. Vibrio chromosomes share common history

    Directory of Open Access Journals (Sweden)

    Gevers Dirk


    Full Text Available Abstract Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history. Conclusions Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA for one chromosome to be applied equally to both chromosomes.

  10. Magnetic fluid equipment for sorting of secondary polyolefins from waste

    NARCIS (Netherlands)

    Rem, P.C.; Di Maio, F.; Hu, B.; Houzeaux, G...; Baltes, L.; Tierean, M.


    The paper presents the researches made on the FP7 project „Magnetic Sorting and Ultrasound Sensor Technologies for Production of High Purity Secondary Polyolefins from Waste” in order to develop a magnetic fluid equipment for sorting of polypropylene (PP) and polyethylene (PE) from polymers mixed wa

  11. Finding all sorting tandem duplication random loss operations

    DEFF Research Database (Denmark)

    Bernt, Matthias; Chen, Kuan Yu; Chen, Ming Chiang


    a theoretical point of view. Of particular interest are sorting TDRLs which are TDRLs that, when applied to a permutation representing a genome, reduce the distance towards another given permutation. The identification of sorting genome rearrangement operations in general is a key ingredient of many algorithms...

  12. Method and set-up for uranium ore sorting

    Energy Technology Data Exchange (ETDEWEB)

    Dragulescu, E.; Ivascu, M.; Popescu, D.; Semenescu, G. (Institutul de Fizica si Inginerie Nucleara, Bucharest (Romania)); Gherea, Gh. (Intreprinderea metalelor rare, Bucuresti (Romania)); Draga, Z.; Funaru, Gh. (Exploatarea miniera Oravita, Oravita (Romania))


    A method was studied for uranium ore sorting. After the discussion of the principle, some particular conditions of the sorting are pointed out. A radiometric assembly is described and some results obtained on the simulator and in industrial conditions are reported.

  13. Tradeoffs Between Branch Mispredictions and Comparisons for Sorting Algorithms

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel


    Branch mispredictions is an important factor affecting the running time in practice. In this paper we consider tradeoffs between the number of branch mispredictions and the number of comparisons for sorting algorithms in the comparison model. We prove that a sorting algorithm using O(dnlog n...

  14. A FORTRAN Computer Program for Q Sort Calculations (United States)

    Dunlap, William R.


    The Q Sort method is a rank order procedure. A FORTRAN program is described which calculates a total value for any group of cases for the items in the Q Sort, and rank orders the items according to this composite value. (Author/JKS)

  15. A Comparison of Card-sorting Analysis Methods

    DEFF Research Database (Denmark)

    Nawaz, Ather


    the recurrent patterns found and thus has consequences for the resulting website design. This paper draws an attention to the choice of card sorting analysis and techniques and shows how it impacts the results. The research focuses on how the same data for card sorting can lead to different website structures...

  16. Feed sorting in dairy cattle: Causes, consequences, and management. (United States)

    Miller-Cushon, E K; DeVries, T J


    Dairy cattle commonly sort total mixed rations, a behavior that influences individual nutrient intake and reduces the nutritive value of the ration left in the bunk across the day. Typical patterns of feed sorting in lactating dairy cows, against longer forage particles, result in greater intake of highly-fermentable carbohydrates and lesser intake of effective fiber than intended, and are associated with reduced rumen pH and altered milk composition. To understand the reason for this behavior and reduce it on-farm, numerous studies have explored the influences of ration characteristics, feeding strategies, and management factors on the expression of feed sorting. In mature cows and young calves, feed sorting is influenced by forage inclusion rate, particle size, and dry matter content. Feeding strategies that increase the time available to manipulate feed-including decreased feeding frequency and increased feeding level-may result in increased feed sorting. The extent of feed sorting is also influenced by a variety of herd-level factors, but variability between individuals in the extent of feed sorting suggests that this behavior may be subject to additional factors, including previous experience and internal state. The development of feed sorting in young calves has been explored in several recent studies, suggesting that early opportunities to sort feed, as provided by access to mixed diets, may encourage the early onset of this behavior and help it persist beyond weaning. Evidence also supports the role of feedback mechanisms that influence this behavior at the individual level. In calves and adult cows, selective consumption of higher-energy ration components may be linked to energy demands, as influenced by the availability of supplemental feed or changing metabolic status. Further, considerable evidence suggests that cattle will adjust patterns of feed sorting in favor of physically effective fiber to attenuate low rumen pH, providing evidence for the role

  17. Sorting Pairs of Points Based on Their Distances

    Directory of Open Access Journals (Sweden)

    Mohammad Farshi


    Full Text Available Sorting data is one of the main problems in computer science which studied vastly and used in several places. In several geometric problems, like problems on point sets or lines in the plane or Euclidean space with higher dimensions, the problem of sorting pairs of points based on the distance (between them is used. Using general sorting algorithms, sorting n 2 distances between n points can be done in O(n2 log n time. Ofcourse, sorting (n2 independent numbers does not have a faster solution, but since we have dependency between numbers in this case, finding a faster algorithm or showing that the problem in this case has O(n2 log n time complexity is interesting. In this paper, we try to answer this question.

  18. Degree of molecular self-sorting in multicomponent systems. (United States)

    Saha, Manik Lal; Schmittel, Michael


    Self-sorting represents the spontaneous and high fidelity self and/or non-self-recognition of two or more related components within a complex mixture. While the effective management of self-sorting principles perceptibly requires some key expertise in molecular programming, at a higher stage of operation it is of supreme interest to guide the process to increasingly higher degrees of self-sorting. In this article, we present the emerging principles of how to guide several components toward formation of self-sorted multicomponent architectures. To provide further guidance in denominating such systems, we suggest to utilise a systematic classification as well as a formula to evaluate their degree of self-sorting (M).

  19. Standard practice for cell sorting in a BSL-3 facility. (United States)

    Perfetto, Stephen P; Ambrozak, David R; Nguyen, Richard; Roederer, Mario; Koup, Richard A; Holmes, Kevin L


    Over the past decade, there has been a rapid growth in the number of BSL-3 and BSL-4 laboratories in the USA and an increase in demand for infectious cell sorting in BSL-3 laboratories. In 2007, the International Society for Advancement of Cytometry (ISAC) Biosafety Committee published standards for the sorting of unfixed cells and is an important resource for biosafety procedures when performing infectious cell sorting. Following a careful risk assessment, if it is determined that a cell sorter must be located within a BSL-3 laboratory, there are a variety of factors to be considered prior to the establishment of the laboratory. This chapter outlines procedures for infectious cell sorting in a BSL-3 environment to facilitate the establishment and safe operation of a BSL-3 cell sorting laboratory. Subjects covered include containment verification, remote operation, disinfection, personal protective equipment (PPE), and instrument-specific modifications for enhanced aerosol evacuation.

  20. Effects of Hoechst33342 staining on the viability and flow cytometric sex-sorting of frozen-thawed ram sperm. (United States)

    Quan, Guo Bo; Ma, Yuan; Li, Jian; Wu, Guo Quan; Li, Dong Jiang; Ni, Yi Na; Lv, Chun Rong; Zhu, Lan; Hong, Qiong Hua


    Cytometric sorting of frozen-thawed sperm can overcome difficulties caused by the unavailability of sorting facilities on farms where semen is collected from male livestock. In order to optimize the cytometric sex-sorting procedure, effects of Hoechst33342 staining on the viability and cytometric sorting efficiency of frozen-thawed ram sperm were evaluated. The frozen-thawed sperm were stained with Hoechst33342 at various dye concentrations (80 μM, 120 μM, 160 μM, 200 μM, 240 μM, or 320 μM) for 45 min to evaluate effects of dye dose. The frozen-thawed sperm were stained with 160 μM Hoechst33342 for various durations (0 min, 15 min, 30 min, 45 min, 60 min, 75 min, or 90 min) to evaluate effects of staining duration. Sperm motility and moving velocity were analyzed using a computer-assisted sperm analysis system (CASAS). Acrosome status, membrane integrity, and distribution of phosphatidylserine (PS) in Hoechst33342-stained sperm were analyzed using flow cytometry after staining with fluorescein isothiocyanate-labeled lectin from pisum sativum (FITC-PSA), Annexin V, or propidium iodide (PI). The fertility of Hoechst33342-stained sperm was analyzed by in vitro fertilization (IVF). A high-speed cell sorter was used to evaluate effects of Hoechst33342 staining on cytometric sex-sorting of frozen-thawed sperm. The motility, moving velocity, membrane integrity, and PS distribution of Hoechst33342-stained sperm were significantly different from that of immediately thawed sperm (Pram sperm. Results of cytometric sorting indicated that frozen-thawed sperm can be efficiently sorted into two sperm populations with X and Y chromosome when the Hoechst33342 concentration was 160 μM. Moreover, when the staining duration was equal to or longer than 45 min, the frozen-thawed sperm can be successfully sorted in the presence of 160μM Hoechst33342. In conclusion, Hoechst33342 staining can detrimentally influence viability of frozen-thawed ram sperm except acrosome and in vitro

  1. Cell sorting using efficient light shaping approaches (United States)

    Bañas, Andrew; Palima, Darwin; Villangca, Mark; Glückstad, Jesper


    Early detection of diseases can save lives. Hence, there is emphasis in sorting rare disease-indicating cells within small dilute quantities such as in the confines of lab-on-a-chip devices. In our work, we use optical forces to isolate red blood cells detected by machine vision. This approach is gentler, less invasive and more economical compared to conventional FACS systems. As cells are less responsive to plastic or glass beads commonly used in the optical manipulation literature, and since laser safety would be an issue in clinical use, we develop efficient approaches in utilizing lasers and light modulation devices. The Generalized Phase Contrast (GPC) method that can be used for efficiently illuminating spatial light modulators or creating well-defined contiguous optical traps is supplemented by diffractive techniques capable of integrating the available light and creating 2D or 3D beam distributions aimed at the positions of the detected cells. Furthermore, the beam shaping freedom provided by GPC can allow optimizations in the beam's propagation and its interaction with the catapulted cells.

  2. Microfluidic-chip platform for cell sorting (United States)

    Malik, Sarul; Balyan, Prerna; Akhtar, J.; Agarwal, Ajay


    Cell sorting and separation are considered to be very crucial preparatory steps for numerous clinical diagnostics and therapeutics applications in cell biology research arena. Label free cell separation techniques acceptance rate has been increased to multifold by various research groups. Size based cell separation method focuses on the intrinsic properties of the cell which not only avoids clogging issues associated with mechanical and centrifugation filtration methods but also reduces the overall cost for the process. Consequentially flow based cell separation method for continuous flow has attracted the attention of millions. Due to the realization of structures close to particle size in micro dimensions, the microfluidic devices offer precise and rapid particle manipulation which ultimately leads to an extraordinary cell separation results. The proposed microfluidic device is fabricated to separate polystyrene beads of size 1 µm, 5 µm, 10 µm and 20 µm. The actual dimensions of blood corpuscles were kept in mind while deciding the particle size of polystyrene beads which are used as a model particles for study.

  3. Help the planet by sorting your waste!

    CERN Multimedia


    Paper and cardboard waste comes in various forms, from newspapers to the toughest cardboard. Every year CERN dispatches about 200 tonnes of paper and cardboard to a recycling plant, but this is still too little when you take into consideration the tonnes of paper and cardboard that are still thrown out as part of ordinary rubbish or are incorrectly sorted into other rubbish skips.   Each office is equipped with a wastepaper bin, and a paper and cardboard container is available near every building. Cardboard boxes should be folded before they are placed in the containers in order to save space. Please note: Here are some sobering statistics: - 2 to 3 tonnes of wood pulp are required to manufacture 1 tonne of paper. - Each tonne of recycled paper means that we can save approximately 15 trees and substantial amounts of the water that is needed to extract cellulose (60 litres of water per kilo of paper). - A production of 100% recycled paper represents a 90% saving in water. - 5000 kWh of e...

  4. "Chromosome": a knowledge-based system for the chromosome classification. (United States)

    Ramstein, G; Bernadet, M


    Chromosome, a knowledge-based analysis system has been designed for the classification of human chromosomes. Its aim is to perform an optimal classification by driving a tool box containing the procedures of image processing, pattern recognition and classification. This paper presents the general architecture of Chromosome, based on a multiagent system generator. The image processing tool box is described from the met aphasic enhancement to the fine classification. Emphasis is then put on the knowledge base intended for the chromosome recognition. The global classification process is also presented, showing how Chromosome proceeds to classify a given chromosome. Finally, we discuss further extensions of the system for the karyotype building.

  5. Guest Editorial: Card sort methodology: An objective measure in rehabilitation research


    Haitham Jahrami, PhD


    Card sort clinical tests such as the Wisconsin Card Sort Test and Activity Card Sort are well known in several clinical practices, including psychiatry, neurology, neuropsychology, and learning disabilities. However, card sort methodology is less famous as a research methodology. This editorial attempts to shed light on the novelty of the card sort methodology and its relevance to rehabilitation research.

  6. Microfluidic EmbryoSort technology: towards in flow analysis, sorting and dispensing of individual vertebrate embryos (United States)

    Fuad, Nurul M.; Wlodkowic, Donald


    The demand to reduce the numbers of laboratory animals has facilitated the emergence of surrogate models such as tests performed on zebrafish (Danio rerio) or African clawed frog's (Xenopus levis) eggs, embryos and larvae. Those two model organisms are becoming increasingly popular replacements to current adult animal testing in toxicology, ecotoxicology and also in drug discovery. Zebrafish eggs and embryos are particularly attractive for toxicological analysis due their size (diameter 1.6 mm), optical transparency, large numbers generated per fish and very straightforward husbandry. The current bottleneck in using zebrafish embryos for screening purposes is, however, a tedious manual evaluation to confirm the fertilization status and subsequent dispensing of single developing embryos to multitier plates to perform toxicity analysis. Manual procedures associated with sorting hundreds of embryos are very monotonous and as such prone to significant analytical errors due to operator's fatigue. In this work, we present a proofof- concept design of a continuous flow embryo sorter capable of analyzing, sorting and dispensing objects ranging in size from 1.5 - 2.5 mm. The prototypes were fabricated in polymethyl methacrylate (PMMA) transparent thermoplastic using infrared laser micromachining. The application of additive manufacturing processes to prototype Lab-on-a-Chip sorters using both fused deposition manufacturing (FDM) and stereolithography (SLA) were also explored. The operation of the device was based on a revolving receptacle capable of receiving, holding and positioning single fish embryos for both interrogation and subsequent sorting. The actuation of the revolving receptacle was performed using a DC motor and/or microservo motor. The system was designed to separate between fertilized (LIVE) and non-fertilized (DEAD) eggs, based on optical transparency using infrared (IR) emitters and receivers.

  7. First results from insemination with sex-sorted semen in dairy heifers in Macedonia

    Directory of Open Access Journals (Sweden)

    Ljupche Kochoski


    Full Text Available Science has been searching for a long time for a reliable method for controlling the sex of mammalian offspring. Recently, the application of specific modern cellular methodologies has led to the development of a flow cytometric system capable of differentiating and separating living X- and Y-chromosome-bearing sperm cells in amounts suitable for AI and therefore, commercialization of this sexing technology. The aim of this work was to present the first results of heifers that introduce bovine AI with sex sorted semen, for the first time in Macedonia. Insemination with sex sorted cryopreserved semen (2x106 spermatozoa per dose imported from the USA was done at two dairy farms in ZK Pelagonija. In total, 74 heifers (Holstein Friesian were inseminated. Inseminations were carried out in a timely manner following a modified OvSynch protocol. During the insemination, the sperm was deposited into the uterine horn ipsi lateral to the ovary where a follicle larger than 1.6 cm was detected by means of transrectal ultrasound examination. Pregnancy was checked by ultrasound on day 30 after the insemination. Overall, the average pregnancy rate in both farms was 43,24% (40,54% and 45,95%, for farm 1 and farm 2, respectively. All pregnant heifers delivered their calves following a normal gestation length (274,3 days in average and of the 32 born calves, 30 (93,75% were female. In conclusion, since the first results from inseminations with sex-sorted semen in dairy heifers in Macedonia are very promising, the introduction of this technique may bring much benefit to the local dairy sector. Average pregnancy rate seems similar with results obtained following ‘regular’ inseminations, notwithstanding the relatively low number of spermatozoa per insemination dose. Due to the latter, we however recommend inseminations only to be carried out by experienced technicians followinga TAI protocol and ultrasound examinations of the ovaries prior to insemination.

  8. Chromosome numbers in Bromeliaceae

    Directory of Open Access Journals (Sweden)

    Cotias-de-Oliveira Ana Lúcia Pires


    Full Text Available The present study reports chromosome numbers of 17 species of Bromeliaceae, belonging to the genera Encholirium, Bromelia, Orthophytum, Hohenbergia, Billbergia, Neoglaziovia, Aechmea, Cryptanthus and Ananas. Most species present 2n = 50, however, Bromelia laciniosa, Orthophytum burle-marxii and O. maracasense are polyploids with 2n = 150, 2n = 100 and 2n = 150, respectively, while for Cryptanthus bahianus, 2n = 34 + 1-4B. B chromosomes were observed in Bromelia plumieri and Hohenbergia aff. utriculosa. The chromosome number of all species was determined for the first time, except for Billbergia chlorosticta and Cryptanthus bahianus. Our data supports the hypothesis of a basic number of x = 25 for the Bromeliaceae family and decreasing aneuploidy in the genus Cryptanthus.

  9. Those amazing dinoflagellate chromosomes

    Institute of Scientific and Technical Information of China (English)



    Dinoflagellates are a very large and diverse group of eukaryotic algae that play a major role in aquatic food webs of both fresh water and marine habitats. Moreover, the toxic members of this group pose a health threat in the form of red tides. Finally, dinoflagellates are of great evolutionary importance,because of their taxonomic position, and their unusual chromosome structure and composition. While the cytoplasm of dinoflagellates is typically eukaryotic, the nucleus is unique when compared to the nucleus of other eukaryotes. More specifically, while the chromosomes of all other eukaryotes contain histones,dinoflagellate chromosomes lack histones completely. There are no known exceptions to this observation: all dinoflagellates lack histones, and all other eukaryotes contain histones. Nevertheless, dinoflagellates remain a relatively unstudied group of eukaryotes.

  10. Sortilin regulates sorting and secretion of Sonic hedgehog. (United States)

    Campbell, Charles; Beug, Shawn; Nickerson, Philip E B; Peng, Jimmy; Mazerolle, Chantal; Bassett, Erin A; Ringuette, Randy; Jama, Fadumo A; Morales, Carlos; Christ, Annabel; Wallace, Valerie A


    Sonic Hedgehog (Shh) is a secreted morphogen that is an essential regulator of patterning and growth. The Shh full-length protein undergoes autocleavage in the endoplasmic reticulum to generate the biologically active N-terminal fragment (ShhN), which is destined for secretion. We identified sortilin (Sort1), a member of the VPS10P-domain receptor family, as a new Shh trafficking receptor. We demonstrate that Sort-Shh interact by performing coimmunoprecipitation and proximity ligation assays in transfected cells and that they colocalize at the Golgi. Sort1 overexpression causes re-distribution of ShhN and, to a lesser extent, of full-length Shh to the Golgi and reduces Shh secretion. We show loss of Sort1 can partially rescue Hedgehog-associated patterning defects in a mouse model that is deficient in Shh processing, and we show that Sort1 levels negatively regulate anterograde Shh transport in axons in vitro and Hedgehog-dependent axon-glial interactions in vivo Taken together, we conclude that Shh and Sort1 can interact at the level of the Golgi and that Sort1 directs Shh away from the pathways that promote its secretion.

  11. Microfluidic droplet sorting using integrated bilayer micro-valves (United States)

    Chen, Yuncong; Tian, Yang; Xu, Zhen; Wang, Xinran; Yu, Sicong; Dong, Liang


    This paper reports on a microfluidic device capable of sorting microfluidic droplets utilizing conventional bilayer pneumatic micro-valves as sorting controllers. The device consists of two micro-valves placed symmetrically on two sides of a sorting area, each on top of a branching channel at an inclined angle with respect to the main channel. Changes in transmitted light intensity, induced by varying light absorbance by each droplet, are used to divert the droplet from the sorting area into one of the three outlet channels. When no valve is activated, the droplet flows into the outlet channel in the direction of the main channel. When one of the valves is triggered, the flexible membrane of valve will first be deflected. Once the droplet leaves the detection point, the deflected membrane will immediately return to its default flattened position, thereby exerting a drawing pressure on the droplet and deviating it from its original streamline to the outlet on the same side as the valve. This sorting method will be particularly suitable for numerous large-scale integrated microfluidic systems, where pneumatic micro-valves are already used. Only few structural modifications are needed to achieve droplet sorting capabilities in these systems. Due to the mechanical nature of diverting energy applied to droplets, the proposed sorting method may induce only minimal interference to biological species or microorganisms encapsulated inside the droplets that may accompany electrical, optical and magnetic-based techniques.

  12. Flow virometric sorting and analysis of HIV quasispecies from plasma (United States)

    Jones, Jennifer C.; Keele, Brandon F.; Jenkins, Lisa M. Miller; Demberg, Thorsten


    Flow cytometry is utilized extensively for cellular analysis, but technical limitations have prevented its routine application for characterizing virus. The recent introduction of nanoscale fluorescence-activated cytometric cell sorting now allows analysis of individual virions. Here, we demonstrate staining and sorting of infectious HIV. Fluorescent antibodies specific for cellular molecules found on budding virions were used to label CCR5-tropic Bal HIV and CXCR4-tropic NL4.3 HIV Env-expressing pseudovirions made in THP-1 cells (monocyte/macrophage) and H9 cells (T cells), respectively. Using a flow cytometer, we resolved the stained virus beyond isotype staining and demonstrated purity and infectivity of sorted virus populations on cells with the appropriate coreceptors. We subsequently sorted infectious simian/human immunodeficiency virus from archived plasma. Recovery was approximately 0.5%, but virus present in plasma was already bound to viral-specific IgG generated in vivo, likely contributing to the low yield. Importantly, using two broadly neutralizing HIV antibodies, PG9 and VRC01, we also sorted virus from archived human plasma and analyzed the sorted populations genetically and by proteomics, identifying the quasispecies present. The ability to sort infectious HIV from clinically relevant samples provides material for detailed molecular, genetic, and proteomic analyses applicable to future design of vaccine antigens and potential development of personalized treatment regimens. PMID:28239654

  13. Efficient Sorting of Free Electron Orbital Angular Momentum

    CERN Document Server

    McMorran, Benjamin J; Lavery, Martin P J


    We propose a method for sorting electrons by orbital angular momentum (OAM). Several methods now exist to prepare electron wavefunctions in OAM states, but no technique has been developed for efficient, parallel measurement of pure and mixed electron OAM states. The proposed technique draws inspiration from the recent demonstration of the sorting of OAM through modal transformation. We show that the same transformation can be performed with electrostatic electron optical elements. Specifically, we show that a charged needle and an array of electrodes perform the transformation and phase correction necessary to sort orbital angular momentum states. This device may enable the analysis of the spatial mode distribution of inelastically scattered electrons.

  14. Chromosomal rearrangement interferes with meiotic X chromosome inactivation


    Homolka, David; Ivanek, Robert; Capkova, Jana; Jansa, Petr; Forejt, Jiri


    Heterozygosity for certain mouse and human chromosomal rearrangements is characterized by the incomplete meiotic synapsis of rearranged chromosomes, by their colocalization with the XY body in primary spermatocytes, and by male-limited sterility. Previously, we argued that such X–autosomal associations could interfere with meiotic sex chromosome inactivation. Recently, supporting evidence has reported modifications of histones in rearranged chromosomes by a process called the meiotic silencin...

  15. Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). (United States)

    Akpinar, Bala A; Lucas, Stuart J; Vrána, Jan; Doležel, Jaroslav; Budak, Hikmet


    Flow cytometric sorting of individual chromosomes and chromosome-based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow-sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNA(L) (ys) and tRNA(M) (et) species, while the nonrepetitive assembly reveals tRNA(A) (la) species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome-specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome-level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor.

  16. An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species. (United States)

    Lin, Ying Chih; Lu, Chin Lung; Chang, Hwan-You; Tang, Chuan Yi


    In the study of genome rearrangement, the block-interchanges have been proposed recently as a new kind of global rearrangement events affecting a genome by swapping two nonintersecting segments of any length. The so-called block-interchange distance problem, which is equivalent to the sorting-by-block-interchange problem, is to find a minimum series of block-interchanges for transforming one chromosome into another. In this paper, we study this problem by considering the circular chromosomes and propose a Omicron(deltan) time algorithm for solving it by making use of permutation groups in algebra, where n is the length of the circular chromosome and delta is the minimum number of block-interchanges required for the transformation, which can be calculated in Omicron(n) time in advance. Moreover, we obtain analogous results by extending our algorithm to linear chromosomes. Finally, we have implemented our algorithm and applied it to the circular genomic sequences of three human vibrio pathogens for predicting their evolutionary relationships. Consequently, our experimental results coincide with the previous ones obtained by others using a different comparative genomics approach, which implies that the block-interchange events seem to play a significant role in the evolution of vibrio species.

  17. Electochemical detection of chromosome translocation

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Dimaki, Maria; Silahtaroglu, Asli;


    Cytogenetics is a study of the cell structure with a main focus on chromosomes content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders and heametological malignancies. Chromosome translocations are structural rearrangements of two...... chromosomes that results in formation of derivative chromosomes with a mixed DNA sequence. The method currently used for their detection is Fluorescent In Situ Hybridization, which requires a use of expensive, fluorescently labeled probes that target the derivative chromosomes. We present here a double...... hybridization approach developed for label-free detection of the chromosome translocations. For specific translocation detection it is necessary to determine that the two DNA sequences forming a derivative chromosome are connected, which is achieved by two subsequent hybridization steps. The electrochemical...

  18. Chromosome Variations And Human Behavior (United States)

    Soudek, D.


    Article focused on the science of cytogenetics, which studied the transmission of the units of heredity called chromosomes, and considered the advantage of proper diagnosis of genetic diseases, treated on the chromosomal level. (Author/RK)

  19. Ring chromosome 13

    DEFF Research Database (Denmark)

    Brandt, C A; Hertz, Jens Michael; Petersen, M B;


    A stillborn male child with anencephaly and multiple malformations was found to have the karyotype 46,XY,r(13) (p11q21.1). The breakpoint at 13q21.1, determined by high resolution banding, is the most proximal breakpoint ever reported in patients with ring chromosome 13. In situ hybridisation...

  20. Chromosomes, cancer and radiosensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Samouhos, E.


    Some specific chromosomal abnormalities are associated with certain cancers. The earliest description of such a specific association is the one of the Philadelphia chromosome and myelogenous leukemia (1960). Other congenital karyotype abnormalities are associated with specific cancers. Examples of these are Down's syndrome with leukemia and Klinefelter's syndrome with male breast cancer. Genetic diseases of increased chromosome breakage, or of defective chromosome repair, are associated with greatly increased cancer incidence. Three such diseases have been recognized: 1) Fanconi's anemia, associated with leukemias and lymphomas, 2) Bloom's syndrome, associated with acute leukemias and lymphosarcoma, and 3) ataxia telangiectasia, associated with Hodgkin's disease, leukemia, and lymphosarcomas. Ten percent of individuals with ataxia telangiectasia will develop one of these neoplasms. Individuals with certain of these syndromes display an unusually high radiosensitivity. Radiation therapy for cancers has been fatal in patients who received as low as 3000 rad. This remarkable radiosensitivity has been quantitated in cell cultures from such cases. Evidence suggests that the apparent sensitivity may reflect subnormal ability to repair radiation damage. The rapid proliferation of information in this field stems from the interdigitation of many disciplines and specialties, including cytogenetics, cell biology, molecular biology, epidemiology, radiobiology, and several others. This paper is intended for clinicians; it presents a structured analytic scheme for correlating and classifying this multidisciplinary information as it becomes available.

  1. The Y Chromosome (United States)

    Offner, Susan


    The Y chromosome is of great interest to students and can be used to teach about many important biological concepts in addition to sex determination. This paper discusses mutation, recombination, mammalian sex determination, sex determination in general, and the evolution of sex determination in mammals. It includes a student activity that…

  2. Why Chromosome Palindromes?

    Directory of Open Access Journals (Sweden)

    Esther Betrán


    Full Text Available We look at sex-limited chromosome (Y or W evolution with particular emphasis on the importance of palindromes. Y chromosome palindromes consist of inverted duplicates that allow for local recombination in an otherwise nonrecombining chromosome. Since palindromes enable intrachromosomal gene conversion that can help eliminate deleterious mutations, they are often highlighted as mechanisms to protect against Y degeneration. However, the adaptive significance of recombination resides in its ability to decouple the evolutionary fates of linked mutations, leading to both a decrease in degeneration rate and an increase in adaptation rate. Our paper emphasizes the latter, that palindromes may exist to accelerate adaptation by increasing the potential targets and fixation rates of incoming beneficial mutations. This hypothesis helps reconcile two enigmatic features of the “palindromes as protectors” view: (1 genes that are not located in palindromes have been retained under purifying selection for tens of millions of years, and (2 under models that only consider deleterious mutations, gene conversion benefits duplicate gene maintenance but not initial fixation. We conclude by looking at ways to test the hypothesis that palindromes enhance the rate of adaptive evolution of Y-linked genes and whether this effect can be extended to palindromes on other chromosomes.

  3. FPGA-based Accelerators for Parallel Data Sort

    Directory of Open Access Journals (Sweden)

    Sklyarov Valery


    Full Text Available The paper is dedicated to parallel data sort based on sorting networks. The proposed methods and circuits have the following characteristics: 1 using two-level parallel comparators in even-odd transition networks with feedback to a register keeping input/intermediate data; 2 parallel merging of many sorted sequences; 3 using even-odd transition networks built from other sorting networks; 4 rational reuse of comparators in different types of networks, namely even-odd transition and for discovering maximum/minimum values. The experiments in FPGA, which were done for up to 16×220 32-bit data items, demonstrate very good results (as fast as 3-5 ns per data item.

  4. Combination of the Sorting Line Priority Polling Control Mechanism

    Directory of Open Access Journals (Sweden)

    Wenxue Ran


    Full Text Available The paper proposed the priority polling control mechanism of the unit material combinations sorting lines, and sorters operating process is understood to be the arrival process of orders, service process of each sorter sorts orders and the conversion process between sorting machines. Control process, sorters of the combined sorting lines are divided into the priority sorters and ordinary sorters, priority sorters use full service control, ordinary sorters use limited service (k = 1, applies the polling service system theory, through the embedded Markov chain and probability generating function to establish the mathematical model of the system, the exact solution of the control mechanism of the polling system model and the first and second characteristic parameters, combined with the actual production priority parameters of orders picking for simulation analysis

  5. Unsupervised Spike Sorting Based on Discriminative Subspace Learning

    CERN Document Server

    Keshtkaran, Mohammad Reza


    Spike sorting is a fundamental preprocessing step for many neuroscience studies which rely on the analysis of spike trains. In this paper, we present two unsupervised spike sorting algorithms based on discriminative subspace learning. The first algorithm simultaneously learns the discriminative feature subspace and performs clustering. It uses histogram of features in the most discriminative projection to detect the number of neurons. The second algorithm performs hierarchical divisive clustering that learns a discriminative 1-dimensional subspace for clustering in each level of the hierarchy until achieving almost unimodal distribution in the subspace. The algorithms are tested on synthetic and in-vivo data, and are compared against two widely used spike sorting methods. The comparative results demonstrate that our spike sorting methods can achieve substantially higher accuracy in lower dimensional feature space, and they are highly robust to noise. Moreover, they provide significantly better cluster separab...

  6. Running worms: C. elegans self-sorting by electrotaxis.

    Directory of Open Access Journals (Sweden)

    Xavier Manière

    Full Text Available The nematode C. elegans displays complex dynamical behaviors that are commonly used to identify relevant phenotypes. Although its maintenance is straightforward, sorting large populations of worms when looking for a behavioral phenotype is difficult, time consuming and hardly quantitative when done manually. Interestingly, when submitted to a moderate electric field, worms move steadily along straight trajectories. Here, we report an inexpensive method to measure worms crawling velocities and sort them within a few minutes by taking advantage of their electrotactic skills. This method allows to quantitatively measure the effect of mutations and aging on worm's crawling velocity. We also show that worms with different locomotory phenotypes can be spatially sorted, fast worms traveling away from slow ones. Group of nematodes with comparable locomotory fitness could then be isolated for further analysis. C. elegans is a growing model for neurodegenerative diseases and using electrotaxis for self-sorting can improve the high-throughput search of therapeutic bio-molecules.

  7. Natural Selection Is a Sorting Process: What Does that Mean? (United States)

    Price, Rebecca M.


    To learn why natural selection acts only on existing variation, students categorize processes as either creative or sorting. This activity helps students confront the misconception that adaptations evolve because species need them.

  8. Using Sorting Networks for Skill Building and Reasoning (United States)

    Andre, Robert; Wiest, Lynda R.


    Sorting networks, used in graph theory, have instructional value as a skill- building tool as well as an interesting exploration in discrete mathematics. Students can practice mathematics facts and develop reasoning and logic skills with this topic. (Contains 4 figures.)

  9. Telomere dysfunction and chromosome instability

    Energy Technology Data Exchange (ETDEWEB)

    Murnane, John P., E-mail: [Department of Radiation Oncology, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143-1331 (United States)


    The ends of chromosomes are composed of a short repeat sequence and associated proteins that together form a cap, called a telomere, that keeps the ends from appearing as double-strand breaks (DSBs) and prevents chromosome fusion. The loss of telomeric repeat sequences or deficiencies in telomeric proteins can result in chromosome fusion and lead to chromosome instability. The similarity between chromosome rearrangements resulting from telomere loss and those found in cancer cells implicates telomere loss as an important mechanism for the chromosome instability contributing to human cancer. Telomere loss in cancer cells can occur through gradual shortening due to insufficient telomerase, the protein that maintains telomeres. However, cancer cells often have a high rate of spontaneous telomere loss despite the expression of telomerase, which has been proposed to result from a combination of oncogene-mediated replication stress and a deficiency in DSB repair in telomeric regions. Chromosome fusion in mammalian cells primarily involves nonhomologous end joining (NHEJ), which is the major form of DSB repair. Chromosome fusion initiates chromosome instability involving breakage-fusion-bridge (B/F/B) cycles, in which dicentric chromosomes form bridges and break as the cell attempts to divide, repeating the process in subsequent cell cycles. Fusion between sister chromatids results in large inverted repeats on the end of the chromosome, which amplify further following additional B/F/B cycles. B/F/B cycles continue until the chromosome acquires a new telomere, most often by translocation of the end of another chromosome. The instability is not confined to a chromosome that loses its telomere, because the instability is transferred to the chromosome donating a translocation. Moreover, the amplified regions are unstable and form extrachromosomal DNA that can reintegrate at new locations. Knowledge concerning the factors promoting telomere loss and its consequences is

  10. [Dicentric Y chromosome]. (United States)

    Abdelmoula, N Bouayed; Amouri, A


    Dicentric Y chromosomes are the most common Y structural abnormalities and their influence on gonadal and somatic development is extremely variable. Here, we report the third comprehensive review of the literature concerning dicentric Y chromosomes reported since 1994. We find 78 new cases for which molecular studies (PCR or FISH) have been widely applied to investigate SRY (68% of cases), GBY, ZFY, RFS4Y, GCY and different genes at AZF region. For dic(Yq), all cases (n = 20) were mosaic for 45,X and 4 of them were also mosaic for a 46,XY cell line. When breakpoints were available (15/20 cases), they were in Yp11. 50% of cases were phenotypic female and 20% phenotypic male while 20% of cases were reported with gonadal dysgenesis. Gonadal histology was defined in 8 cases but only in one case, gonadal tissu was genetically investigated because of gonadoblastoma. For dic(Yp) (n = 55), mosaicism concerned only 45,X cell line and was found in 50 cases while the remainder five cases were homogeneous. When breakpoints were available, it was at Yq11 in 50 cases and at Yq12 in two cases. 54% of cases were phenotypic female, 26% were phenotypic male and 18% were associated with genitalia ambiguous. SRY was analyzed in 33 cases, sequenced in 9 cases and was muted in only one case. Gonads were histologically explored in 34 cases and genetically investigated in 8 cases. Gonadoblastoma was found in only two cases. Through this review, it seems that phenotype-genotype correlations are still not possible and that homogeneous studies of dic(Y) in more patients using molecular tools for structural characterization of the rearranged Y chromosome and assessment of mosaicism in many organs are necessary to clarify the basis of the phenotypic heterogeneity of dicentric Y chromosomes and then to help phenotypic prediction of such chromosome rearrangement.

  11. Dynamics of X Chromosome Inactivation

    NARCIS (Netherlands)

    F. Loos (Friedemann)


    markdownabstract__Abstract__ Dosage compensation evolved to account for the difference in expression of sex chromosome-linked genes. In mammals dosage compensation is achieved by inactivation of one X chromosome during early female embryogenesis in a process called X chromosome inactivation (XCI).

  12. The chromosomes of the Didelphidae (Marsupialia) and their evolutionary significance (United States)

    Reig, O.; Gardner, A.L.; Bianchi, N.O.; Patton, J.L.


    One hundred and seventy-seven specimens of American didelphids, representing 9 genera and 22 species have been studied for their chromosomal constitution. Didelphids are very conservative in chromosomal complements. All of the studied species can be sorted into one of three kinds of karyotypes: 2n= 14 (three species of Didelphis, one of Lutreolina, two of Philander, and one of Chironectes), 2n = 14 (eight species of Marmosa, one of Metachirus, three of Caluromys, and one of Dromiciops), and 2n= 18 (three species of Monodelphis). These karyotypes are stable, showing only minor variations within each basic pattern. It is concluded that chromosomals evolution in the Didelphidae proceededs from low numbers to higher numbers by a process of centromeric fissioning complemented by some pericentric inversions and/or translocations. The pattern of karyotypic stability is consistent with bradytely at the organismic level of evolution. This is explained by a low rate of regulatory genetic evolution promoted by epistatic selection favouring the retention of chromosomal arrangements highly advantageous for overall adaptation.


    Institute of Scientific and Technical Information of China (English)

    万建; 国强; 宋文明


    With the increase of complexity of electromagnetic environment and continuous appearance of advanced system radars ,signals received by radar reconnaissance receivers become even more intensive and complex .There-fore ,traditional radar sorting methods based on neural network algorithms and support vector machine (SVM ) cannot process them effectively .Aiming at solving this problem ,a novel radar signal sorting method based on the cloud model theory and the geometric covering algorithm is proposed .By applying the geometric covering algo-rithm to divide input signals into different covering domains based on their distribution characteristics ,the method can overcome a typical problem that it is easy for traditional sorting algorithms to fall into the local extrema due to the use of complex nonlinear equation to describe input signals .The method uses the cloud model to describe the membership degree between signals to be sorted and their covering domains ,thus it avoids the disadvantage that traditional sorting methods based on hard clustering cannot deinterleave the signal samples with overlapped param-eters .Experimental results show that the presented method can effectively sort advanced system radar signals with overlapped parameters in complex electromagnetic environment .

  14. Random walk models of worker sorting in ant colonies. (United States)

    Sendova-Franks, Ana B; Van Lent, Jan


    Sorting can be an important mechanism for the transfer of information from one level of biological organization to another. Here we study the algorithm underlying worker sorting in Leptothorax ant colonies. Worker sorting is related to task allocation and therefore to the adaptive advantages associated with an efficient system for the division of labour in ant colonies. We considered four spatially explicit individual-based models founded on two-dimensional correlated random walk. Our aim was to establish whether sorting at the level of the worker population could occur with minimal assumptions about the behavioural algorithm of individual workers. The behaviour of an individual worker in the models could be summarized by the rule "move if you can, turn always". We assume that the turning angle of a worker is individually specific and negatively dependent on the magnitude of an internal parameter micro which could be regarded as a measure of individual experience or task specialization. All four models attained a level of worker sortedness that was compatible with results from experiments onLeptothorax ant colonies. We found that the presence of a sorting pivot, such as the nest wall or an attraction force towards the centre of the worker population, was crucial for sorting. We make a distinction between such pivots and templates and discuss the biological implications of their difference.

  15. Chromosomal breakpoints characterization of two supernumerary ring chromosomes 20. (United States)

    Guediche, N; Brisset, S; Benichou, J-J; Guérin, N; Mabboux, P; Maurin, M-L; Bas, C; Laroudie, M; Picone, O; Goldszmidt, D; Prévot, S; Labrune, P; Tachdjian, G


    The occurrence of an additional ring chromosome 20 is a rare chromosome abnormality, and no common phenotype has been yet described. We report on two new patients presenting with a supernumerary ring chromosome 20 both prenatally diagnosed. The first presented with intrauterine growth retardation and some craniofacial dysmorphism, and the second case had a normal phenotype except for obesity. Conventional cytogenetic studies showed for each patient a small supernumerary marker chromosome (SMC). Using fluorescence in situ hybridization, these SMCs corresponded to ring chromosomes 20 including a part of short and long arms of chromosome 20. Detailed molecular cytogenetic characterization showed different breakpoints (20p11.23 and 20q11.23 for Patient 1 and 20p11.21 and 20q11.21 for Patient 2) and sizes of the two ring chromosomes 20 (13.6 Mb for case 1 and 4.8 Mb for case 2). Review of the 13 case reports of an extra r(20) ascertained postnatally (8 cases) and prenatally (5 cases) showed varying degrees of phenotypic abnormalities. We document a detailed molecular cytogenetic chromosomal breakpoints characterization of two cases of supernumerary ring chromosomes 20. These results emphasize the need to characterize precisely chromosomal breakpoints of supernumerary ring chromosomes 20 in order to establish genotype-phenotype correlation. This report may be helpful for prediction of natural history and outcome, particularly in prenatal diagnosis.

  16. Familial complex chromosomal rearrangement resulting in a recombinant chromosome. (United States)

    Berend, Sue Ann; Bodamer, Olaf A F; Shapira, Stuart K; Shaffer, Lisa G; Bacino, Carlos A


    Familial complex chromosomal rearrangements (CCRs) are rare and tend to involve fewer breakpoints and fewer chromosomes than CCRs that are de novo in origin. We report on a CCR identified in a child with congenital heart disease and dysmorphic features. Initially, the child's karyotype was thought to involve a straightforward three-way translocation between chromosomes 3, 8, and 16. However, after analyzing the mother's chromosomes, the mother was found to have a more complex rearrangement that resulted in a recombinant chromosome in the child. The mother's karyotype included an inverted chromosome 2 and multiple translocations involving chromosomes 3, 5, 8, and 16. No evidence of deletion or duplication that could account for the clinical findings in the child was identified.

  17. An Evaluation of the Critical Factors Affecting the Efficiency of Some Sorting Techniques

    Directory of Open Access Journals (Sweden)

    Olabiyisi S.O.


    Full Text Available Sorting allows information or data to be put into a meaningful order. As efficiency is a major concern of computing, data are sorted in order to gain the efficiency in retrieving or searching tasks. The factors affecting the efficiency of shell, Heap, Bubble, Quick and Merge sorting techniques in terms of running time, memory usage and the number of exchanges were investigated. Experiment was conducted for the decision variables generated from algorithms implemented in Java programming and factor analysis by principal components of the obtained experimental data was carried out in order to estimate the contribution of each factor to the success of the sorting algorithms. Further statistical analysis was carried out to generate eigenvalue of the extracted factor and hence, a system of linear equations which was used to estimate the assessment of each factor of the sorting techniques was proposed. The study revealed that the main factor affecting these sorting techniques was time taken to sort. It contributed 97.842%, 97.693%, 89.351%, 98.336% and 90.480% for Bubble sort, Heap sort, Merge sort, Quick sort and Shell sort respectively. The number of swap came second contributing 1.587% for Bubble sort, 2.305% for Heap sort, 10.63% for Merge sort, 1.643% for Quick sort and 9.514% for Shell sort. The memory used was the least of the factors contributing negligible percentage for the five sorting techniques. It contributed 0.571% for Bubble sort, 0.002% for Heap sort, 0.011% for Merge sort, 0.021% for Quick sort and 0.006% for Shell sort.

  18. Chromosomal localization of the human apolipoprotein B gene and detection of homologous RNA in monkey intestine

    Energy Technology Data Exchange (ETDEWEB)

    Deeb, S.S.; Disteche, C.; Motulsky, A.G.; Lebo, R.V.; Kan, Y.W.


    A cDNA clone of the human apolipoprotein B-100 was used as a hybridization probe to detect homologous sequences in both flow-sorted and in situ metaphase chromosomes. The results indicate that the gene encoding this protein is on the distal end of the short arm of chromosome 2 (2p23-2p24). RNA isolated from monkey small intestine contained sequences (6.5 and 18 kilobases) homologous to the cDNA of apolipoprotein B-100. These results are consistent with the hypothesis that one gene codes for both the intestinal (B-48) and the hepatic (B-100) forms.

  19. Microfluidic train station: highly robust and multiplexable sorting of droplets on electric rails. (United States)

    Frenzel, Daniel; Merten, Christoph A


    Fluorescence-activated droplet sorting (FADS) has become a widely used technique for high-throughput screening applications. However, existing methods are very sensitive to fluctuating flow rates at the sorting junction, which can be caused by the pulsing effects of mechanical pumps, droplet aggregates or the accumulation of precipitates during lengthy biological screening applications. Furthermore, existing sorting devices allow only 2-way sorting. We present here a dielectrophoretic sorting system in which the droplets are sorted along multiple electrode pairs that run parallel to the channels. This enables highly reliable sorting (no errors were detected for more than 2000 sorting events) even when inverting the relative flow rates at a 2-way sorting junction from 80 : 20 to 20 : 80. Furthermore, our toolbox is scalable: we demonstrate on the example of a triple-colour sorting experiment with a total of four decoupled electrodes that multi-way sorting is feasible.

  20. Chromosome 19 International Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Pericak-Vance, M.A. (Duke Univ., Durham, NC (United States). Medical Center); Ropers, H.H. (Univ. Hospital Nijmegen, (The Netherlands). Dept. of Human Genetics); Carrano, A.J. (Lawrence Livermore National Lab., CA (United States))


    The Second International Workshop on Human Chromosome 19 was hosted on January 25 and 26, 1992, by the Department of Human Genetics, University Hospital Nijmegen, The Netherlands, at the 'Meerdal Conference Center'. The workshop was supported by a grant from the European Community obtained through HUGO, the Dutch Research Organization (NWO) and the Muscular Dystrophy Association (MDA). Travel support for American participants was provided by the Department of Energy. The goals of this workshop were to produce genetic, physical and integrated maps of chromosome 19, to identify inconsistencies and gaps, and to discuss and exchange resources and techniques available for the completion of these maps. The second day of the meeting was largely devoted to region or disease specific efforts. In particular, the meeting served as a platform for assessing and discussing the recent progress made into the molecular elucidation of myotonic dystrophy.

  1. Human Chromosome 21: Mapping of the chromosomes and cloning of cDNAs

    Energy Technology Data Exchange (ETDEWEB)

    Antonarakis, S.E.


    The objective of the research funded by DOE grant DE-FG02-89ER60857 from 6/15/89 to 8/31/91 was to contribute to the physical mapping of human chromosome 21 (HC21) by cloning large fragments of DNA into Yeast Artificial Chromosomes (YACs) and identify YACs that map on HC21. A total of 54 sequence tagged sites (STS) have been developed and mapped in our laboratory to HC21 and can be used as initial reference points for YAC identification and construction of overlapping clones. A small YAC library was constructed which is HC21 specific. DNA from somatic cell hybrid WAV17 or from flow-sorted HC21 was partially digested with EcoRI, ligated into vectors PJS97, PJS98, and YACs have been obtained with average size insert of more than 300 kb. This library has been deposited in D. Patterson's lab for the Joint YAC screening effort. Additional YAC libraries from ICI Pharmaceuticals or from Los Alamos National Laboratories have been screened with several STS and positive YACs have been identified. Work in progress includes screening of YAC libraries in order to construct overlapping clones, characterization of the cloning ends of YACs, characterization of additional STS and cloning of HC21 specific cDNAs. 15 refs., 2 figs., 5 tabs.

  2. Neuronal spike sorting based on radial basis function neural networks

    Directory of Open Access Journals (Sweden)

    Taghavi Kani M


    Full Text Available "nBackground: Studying the behavior of a society of neurons, extracting the communication mechanisms of brain with other tissues, finding treatment for some nervous system diseases and designing neuroprosthetic devices, require an algorithm to sort neuralspikes automatically. However, sorting neural spikes is a challenging task because of the low signal to noise ratio (SNR of the spikes. The main purpose of this study was to design an automatic algorithm for classifying neuronal spikes that are emitted from a specific region of the nervous system."n "nMethods: The spike sorting process usually consists of three stages: detection, feature extraction and sorting. We initially used signal statistics to detect neural spikes. Then, we chose a limited number of typical spikes as features and finally used them to train a radial basis function (RBF neural network to sort the spikes. In most spike sorting devices, these signals are not linearly discriminative. In order to solve this problem, the aforesaid RBF neural network was used."n "nResults: After the learning process, our proposed algorithm classified any arbitrary spike. The obtained results showed that even though the proposed Radial Basis Spike Sorter (RBSS reached to the same error as the previous methods, however, the computational costs were much lower compared to other algorithms. Moreover, the competitive points of the proposed algorithm were its good speed and low computational complexity."n "nConclusion: Regarding the results of this study, the proposed algorithm seems to serve the purpose of procedures that require real-time processing and spike sorting.

  3. Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting. (United States)

    Li, Tangliang; O'Brien, Patricia C M; Biltueva, Larisa; Fu, Beiyuan; Wang, Jinhuan; Nie, Wenhui; Ferguson-Smith, Malcolm A; Graphodatsky, Alexander S; Yang, Fengtang


    With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: (1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; (2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks (Tamias sibiricus ), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (orde Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

  4. A Sort-Last Rendering System over an Optical Backplane

    Directory of Open Access Journals (Sweden)

    Yasuhiro Kirihata


    Full Text Available Sort-Last is a computer graphics technique for rendering extremely large data sets on clusters of computers. Sort-Last works by dividing the data set into even-sized chunks for parallel rendering and then composing the images to form the final result. Since sort-last rendering requires the movement of large amounts of image data among cluster nodes, the network interconnecting the nodes becomes a major bottleneck. In this paper, we describe a sort-last rendering system implemented on a cluster of computers whose nodes are connected by an all-optical switch. The rendering system introduces the notion of the Photonic Computing Engine, a computing system built dynamically by using the optical switch to create dedicated network connections among cluster nodes. The sort-last volume rendering algorithm was implemented on the Photonic Computing Engine, and its performance is evaluated. Prelimi- nary experiments show that performance is affected by the image composition time and average payload size. In an attempt to stabilize the performance of the system, we have designed a flow control mechanism that uses feedback messages to dynamically adjust the data flow rate within the computing engine.

  5. Stigmergy, self-organization, and sorting in collective robotics. (United States)

    Holland, O; Melhuish, C


    Many structures built by social insects are the outcome of a process of self-organization, in which the repeated actions of the insects interact over time with the changing physical environment to produce a characteristic end state. A major mediating factor is stigmergy, the elicitation of specific environment-changing behaviors by the sensory effects of local environmental changes produced by previous behavior. A typical task involving stigmergic self-organization is brood sorting: Many ant species sort their brood so that items at similar stages of development are grouped together and separated from items at different stages of development. This article examines the operation of stigmergy and self-organization in a homogeneous group of physical robots, in the context of the task of clustering and sorting Frisbees of two different types. Using a behavioral rule set simpler than any yet proposed for ant sorting, and having no capacity for spatial orientation or memory, the robots are able to achieve effective clustering and sorting showing all the signs of self-organization. It is argued that the success of this demonstration is crucially dependent on the exploitation of real-world physics, and that the use of simulation alone to investigate stigmergy may fail to reveal its power as an evolutionary option for collective life forms.

  6. Mechanically robust microfluidics and bulk wave acoustics to sort microparticles (United States)

    Dauson, Erin R.; Gregory, Kelvin B.; Greve, David W.; Healy, Gregory P.; Oppenheim, Irving J.


    Sorting microparticles (or cells, or bacteria) is significant for scientific, medical and industrial purposes. Research groups have used lithium niobate SAW devices to produce standing waves, and then to align microparticles at the node lines in polydimethylsiloxane (PDMS, silicone) microfluidic channels. The "tilted angle" (skewed) configuration is a recent breakthrough producing particle trajectories that cross multiple node lines, making it practical to sort particles. However, lithium niobate wafers and PDMS microfluidic channels are not mechanically robust. We demonstrate "tilted angle" microparticle sorting in novel devices that are robust, rapidly prototyped, and manufacturable. We form our microfluidic system in a rigid polymethyl methacrylate (PMMA, acrylic) prism, sandwiched by lead-zirconium-titanate (PZT) wafers, operating in through-thickness mode with inertial backing, that produce standing bulk waves. The overall configuration is compact and mechanically robust, and actuating PZT wafers in through-thickness mode is highly efficient. Moving to this novel configuration introduced new acoustics questions involving internal reflections, but we show experimental images confirming the intended nodal geometry. Microparticles in "tilted angle" devices display undulating trajectories, where deviation from the straight path increases with particle diameter and with excitation voltage to create the mechanism by which particles are sorted. We show a simplified analytical model by which a "phase space" is constructed to characterize effective particle sorting, and we compare our experimental data to the predictions from that simplified model; precise correlation is not expected and is not observed, but the important physical trends from the model are paralleled in the measured particle trajectories.

  7. An Exploratory Study of Critical Factors Affecting the Efficiency of Sorting Techniques (Shell, Heap and Treap)

    CERN Document Server

    Folorunso, Olusegun; Salako, Oluwatimilehin


    The efficiency of sorting techniques has a significant impact on the overall efficiency of a program. The efficiency of Shell, Heap and Treap sorting techniques in terms of both running time and memory usage was studied, experiments conducted and results subjected to factor analysis by SPSS. The study revealed the main factor affecting these sorting techniques was time taken to sort.

  8. "Clothed in triple blues": sorting out the Italian blues. (United States)

    Bimler, David; Uusküla, Mari


    Cross-cultural comparisons of color perception and cognition often feature versions of the "similarity sorting" procedure. By interpreting the assignment of two color samples to different groups as an indication that the dissimilarity between them exceeds some threshold, sorting data can be regarded as low-resolution similarity judgments. Here we analyze sorting data from speakers of Italian, Russian, and English, applying multidimensional scaling to delineate the boundaries between perceptual categories while highlighting differences between the three populations. Stimuli were 55 color swatches, predominantly from the blue region. Results suggest that at least two Italian words for "blue" are basic, a similar situation to Russian, in contrast to English where a single "blue" term is basic.

  9. Scalable orbital-angular-momentum sorting without destroying photon states

    CERN Document Server

    Wang, Fang-Xiang; Yin, Zhen-Qiang; Wang, Shuang; Guo, Guang-Can; Han, Zheng-Fu


    Single photons with orbital angular momentum (OAM) have attracted substantial attention from researchers. A single photon can carry infinite OAM values theoretically. Thus, OAM photon states have been widely used in quantum information and fundamental quantum mechanics. Although there have been many methods for sorting quantum states with different OAM values, the nondestructive and efficient sorter of high-dimensional OAM remains a fundamental challenge. Here, we propose a scalable OAM sorter which can categorize different OAM states simultaneously, meanwhile, preserving both OAM and spin angular momentum. Fundamental elements of the sorter are composed of symmetric multiport beam splitters (BSs) and Dove prisms with cascading structure, which in principle can be flexibly and effectively combined to sort arbitrarily high-dimensional OAM photons. The scalable structures proposed here greatly reduce the number of BSs required for sorting high-dimensional OAMstates. In view of the nondestructive and extensible ...

  10. Sorting of bending magnets for the SSRF booster

    Institute of Scientific and Technical Information of China (English)

    HOU Jie; LIU Gui-Min; LI Hao-Hu; ZHANG Man-Zhou


    The Shanghai Synchrotron Radiation Facility(SSRF)booster ring,a full energy injector for the storage ring,is deigned to accelerate the electron beam energy from 150MeV to 3.5GeV that demands high extraction efficiency at the extraction energy with low beam loss rate when electrons are ramping.Closed orbit distortion(COD)caused by bending magnet field uniformity errors which affects the machine performance harmfully could be effectively reduced by bending magnet location sorting.Considering the affections of random errors in measurement,both ideal sorting and realistic sorting are studied based on measured bending magnet field uniformity errors and one reasonable combination of bending magnets which can reduce the horizontal COD by a factor of 5is given as the final installation sequence of the booster bending magnets in this paper.

  11. Sorting of bending magnets for the SSRF booster (United States)

    Hou, Jie; Liu, Gui-Min; Li, Hao-Hu; Zhang, Man-Zhou


    The Shanghai Synchrotron Radiation Facility (SSRF)booster ring, a full energy injector for the storage ring, is deigned to accelerate the electron beam energy from 150 MeV to 3.5 GeV that demands high extraction efficiency at the extraction energy with low beam loss rate when electrons are ramping. Closed orbit distortion (COD) caused by bending magnet field uniformity errors which affects the machine performance harmfully could be effectively reduced by bending magnet location sorting. Considering the affections of random errors in measurement, both ideal sorting and realistic sorting are studied based on measured bending magnet field uniformity errors and one reasonable combination of bending magnets which can reduce the horizontal COD by a factor of 5 is given as the final installation sequence of the booster bending magnets in this paper. Supported by SSRF Project

  12. Sorting, Searching, and Simulation in the MapReduce Framework

    DEFF Research Database (Denmark)

    Goodrich, Michael T.; Sitchinava, Nodari; Zhang, Qin


    usefulness of our approach by designing and analyzing efficient MapReduce algorithms for fundamental sorting, searching, and simulation problems. This study is motivated by a goal of ultimately putting the MapReduce framework on an equal theoretical footing with the well-known PRAM and BSP parallel...... models, which would benefit both the theory and practice of MapReduce algorithms. We describe efficient MapReduce algorithms for sorting, multi-searching, and simulations of parallel algorithms specified in the BSP and CRCW PRAM models. We also provide some applications of these results to problems...... in parallel computational geometry for the MapReduce framework, which result in efficient MapReduce algorithms for sorting, 2- and 3-dimensional convex hulls, and fixed-dimensional linear programming. For the case when mappers and reducers have a memory/message-I/O size of M = (N), for a small constant > 0...

  13. Particle migration and sorting in microbubble streaming flows. (United States)

    Thameem, Raqeeb; Rallabandi, Bhargav; Hilgenfeldt, Sascha


    Ultrasonic driving of semicylindrical microbubbles generates strong streaming flows that are robust over a wide range of driving frequencies. We show that in microchannels, these streaming flow patterns can be combined with Poiseuille flows to achieve two distinctive, highly tunable methods for size-sensitive sorting and trapping of particles much smaller than the bubble itself. This method allows higher throughput than typical passive sorting techniques, since it does not require the inclusion of device features on the order of the particle size. We propose a simple mechanism, based on channel and flow geometry, which reliably describes and predicts the sorting behavior observed in experiment. It is also shown that an asymptotic theory that incorporates the device geometry and superimposed channel flow accurately models key flow features such as peak speeds and particle trajectories, provided it is appropriately modified to account for 3D effects caused by the axial confinement of the bubble.

  14. A microfluidic device to sort capsules by deformability

    CERN Document Server

    Zhu, L; Mitra, Dhrubaditya; Brandt, Luca


    Guided by extensive numerical simulations, we propose a microfluidic device that can sort elastic capsules by their deformability. The device consists of a duct embedded with a semi-cylindrical obstacle, and a diffuser which further enhances the sorting capability. We demonstrate that the device can operate reasonably well under changes in the initial position of the the capsule. The efficiency of the device remains essentially unaltered under small changes of the obstacle shape (from semi-circular to semi-elliptic cross-section). Confinement along the direction perpendicular to the plane of the device increases its efficiency. This work is the first numerical study of cell sorting by a realistic microfluidic device.

  15. Cholesterol-induced protein sorting: an analysis of energetic feasibility

    DEFF Research Database (Denmark)

    Lundbaek, J A; Andersen, O S; Werge, T;


    transmembrane domain (TMD). M. S. Bretscher and S. Munro (SCIENCE: 261:1280-1281, 1993) therefore proposed a physical sorting mechanism based on the hydrophobic match between the proteins' TMD and the bilayer thickness, in which cholesterol would regulate protein sorting by increasing the lipid bilayer...... thickness. In this model, Golgi proteins with short TMDs would be excluded from cholesterol-enriched domains (lipid rafts) that are incorporated into transport vesicles destined for the plasma membrane. Although attractive, this model remains unproven. We therefore evaluated the energetic feasibility...... thickness per se, however, have only a modest effect on sorting; the major effect arises because cholesterol changes also the bilayer material properties, which augments the energetic penalty for incorporating short TMDs into cholesterol-enriched domains. We conclude that cholesterol-induced changes...

  16. Intraspecific chromosome variability

    Directory of Open Access Journals (Sweden)

    N Dubinin


    Full Text Available (Editorial preface. The publication is presented in order to remind us of one of dramatic pages of the history of genetics. It re-opens for the contemporary reader a comprehensive work marking the priority change from plant cytogenetics to animal cytogenetics led by wide population studies which were conducted on Drosophila polytene chromosomes. The year of the publication (1937 became the point of irretrievable branching between the directions of Old World and New World genetics connected with the problems of chromosome variability and its significance for the evolution of the species. The famous book of T. Dobzhansky (1937 was published by Columbia University in the US under the title “Genetics and the origin of species”, and in the shadow of this American ‘skybuilding’ all other works grew dim. It is remarkable that both Dobzhansky and Dubinin come to similar conclusions about the role of chromosomes in speciation. This is not surprising given that they both might be considered as representatives of the Russian genetic school, by their birth and education. Interestingly, Dobzhansky had never referred to the full paper of Dubinin et al. (1937, though a previous short communication in Nature (1936 was included together with all former papers on the related subject. In full, the volume of the original publication printed in the Biological Journal in Moscow comprised 47 pages, in that number 41 pages of the Russian text accompanied by 16 Figs, a table and reference list, and, above all, 6 pages of the English summary. This final part in English is now reproduced in the authors’ version with the only addition being the reference list in the originally printed form.

  17. Chromosome assortment in Saccharum. (United States)

    Al-Janabi, S M; Honeycutt, R J; Sobral, B W


    Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum 'SES 208' and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum 'LA Purple' and Saccharum robustum ' Mol 5829'. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.

  18. Basic Study on Color Sorting of Fresh Market Tomatoes


    Mohri, Kentaro; UMEDA, Shigeo; TSURUMI, Gaku


    The surface colors of tomatoes are one of decision factor for the ripeness rate of fruits, and that is mainly graded by the human sense in fact. The color sorting based on the surface colors of tomatoes was attemped by using an opto-electronic system consisting of the color sensors. The sample tomatoes of each ripeness rate were prepared and tested by the color sorting system. As the ripeness rate of tomatoes develops from unripe to ripe, the surface colors change from green to pink or red. W...

  19. Characterization of color texture: color texture based sorting of tiles (United States)

    Bourada, Y.; Lafon, Dominique; Eterradossi, O.


    Many materials used by the building industry show a color texture which affects the product commercial value. This texture can be seen as the spatial arrangement of regions of acceptable color differences. This work describes an appearance based automated sorting via color texture analysis, using ceramic tiles as example. Textural analysis of the tiles digital images expressed in CIEL*a*b* color system is performed through the analysis of intrinsic features of each region and relationships between regions. Results obtained through the automated process are compared to a visual sorting which leads to calculation of application dependant color and texture tolerances.

  20. Decision trees with minimum average depth for sorting eight elements

    KAUST Repository

    AbouEisha, Hassan


    We prove that the minimum average depth of a decision tree for sorting 8 pairwise different elements is equal to 620160/8!. We show also that each decision tree for sorting 8 elements, which has minimum average depth (the number of such trees is approximately equal to 8.548×10^326365), has also minimum depth. Both problems were considered by Knuth (1998). To obtain these results, we use tools based on extensions of dynamic programming which allow us to make sequential optimization of decision trees relative to depth and average depth, and to count the number of decision trees with minimum average depth.

  1. Excitation-energy sorting in superfluid fission dynamics

    Directory of Open Access Journals (Sweden)

    Schmidt K.-H.


    Full Text Available It is now well established that at moderate excitation energies the nucleus temperature does not vary with increasing excitation energy. We show that, as a consequence, two nuclei with different temperatures brought into contact show a rather surprising energy-sorting mechanism where the hotter nucleus transfers all its excitation energy to the colder one. The scission configuration of the fission process offers a unique possibility to observe this phenomenon. The energy-sorting mechanism is clearly reflected by the mean number of prompt neutrons as a function of the fragment mass and by the dependence of the local even-odd effect with mass asymmetry.

  2. Wisconsin card sorting test: a new global score, with Italian norms, and its relationship with the Weigl sorting test. (United States)

    Laiacona, M; Inzaghi, M G; De Tanti, A; Capitani, E


    The Wisconsin card sorting test and the Weigl test are two neuropsychological tools widely used in clinical practice to assess frontal lobe functions. In this study we present norms useful for Italian subjects aged from 15 to 85 years, with 5-17 years of education. Concerning the Wisconsin card sorting test, a new measure of global efficiency (global score) is proposed as well as norms for some well known qualitative aspects of the performance, i.e. perseverative responses, failure to maintain the set and non-perseverative errors. In setting normative values, we followed a statistical methodology (equivalent scores) employed in Italy for other neuropsychological tests, in order to favour the possibility of comparison among these tests. A correlation study between the global score of the Wisconsin card sorting test and the score on the Weigl test was carried out and it emerges that some cognitive aspects are not overlapping in these two measures.

  3. Topographic control of sorted circle morphology on Svalbard (United States)

    Voigt, Joana; Hauber, Ernst; Reiss, Dennis; Hiesinger, Harald; Johnsson, Andreas; van Gasselt, Stephan; Balme, Matt; Head, Jim; de Verra, Jean-Pierre; Steinbrügge, Gregor; Jaumann, Ralf


    Patterned ground is a typical phenomenon in polar, subpolar and alpine regions [1]. As it is commonly (but not necessarily!) related to freeze-thaw cycles, its presence on Mars could possibly point to locations and periods where and when liquid water existed in the recent past [2]. Sorted circles are a class of patterned ground that was tentatively identified in Elysium Planitia (Mars) [3], but this interpretation has been challenged on the basis of physical considerations [4]. Without direct access to potential patterned ground on Mars, the analysis of terrestrial analogues can inform the interpretation of Martian landforms. Svalbard (Norway) offers a wide variety of permafrost features that are morphologically analogous to Martian cold-climate landforms [5]. It hosts some of the best examples of sorted circles on Earth, which are located on the westernmost tip of Brøgger peninsula, on a broad strand flat that is characterized by a series of postglacial beach ridges [6]. Here we report on our analysis of sorted circle morphology (especially their plan-view shape, i.e. their "roundness" or ellipticity) and its correlation with local topography (slopes, curvature). Sorted circle morphology was determined from HRSC-AX images (for details on the flight campaign and image properties see ref [5]) and through field work. Topographic information comes from a 50 cm gridded DEM derived from HRSC-AX stereo images. We measured sorted circle morphology (ellipticity, azimuth of major axis) along a WNW-ESE traverse that runs from the inland towards the sea and is oriented perpendicular to the local beach ridge trend. Selected areas with homogeneous sorted circle appearance were visually mapped, and compared to the average slope, aspect, and the calculated topographic wetness index (TWI). Furthermore the whole traverse was classified into four different morphologies of the sorted patterned ground (sorted circles, sorted "ellipses", sorted nets and areas without patterned ground

  4. In the shadow of phylogenetic uncertainty: the recent diversification of Lysandra butterflies through chromosomal change. (United States)

    Talavera, Gerard; Lukhtanov, Vladimir A; Rieppel, Lukas; Pierce, Naomi E; Vila, Roger


    The phylogeny of the butterfly genus Lysandra (Lycaenidae, Polyommatinae) has been intractable using both molecular and morphological characters, which could be a result of speciation due to karyotype instability. Here we reconstruct the phylogeny of the group using multi-locus coalescent-based methods on seven independent genetic markers. While the genus is ca. 4.9 Mya old, the diversification of the extant lineages was extremely recent (ca. 1.5 Mya) and involved multiple chromosomal rearrangements. We find that relationships are uncertain due to both incomplete lineage sorting and hybridization. Minimizing the impact of reticulation in inferring the species tree by testing for mitochondrial introgression events yields a partially resolved tree with three main supported clades: L. punctifera+L. bellargus, the corydonius taxa, and L. coridon+the Iberian taxa, plus three independent lineages without apparently close relatives (L. ossmar, L. syriaca and L. dezina). Based on these results and new karyotypic data, we propose a rearrangement recognizing ten species within the genus. Finally, we hypothesize that chromosomal instability may have played a crucial role in the Lysandra recent diversification. New chromosome rearrangements might be fixed in populations after severe bottlenecks, which at the same time might promote rapid sorting of neutral molecular markers. We argue that population bottlenecks might be a prerequisite for chromosomal speciation in this group.

  5. Chromosome Connections: Compelling Clues to Common Ancestry (United States)

    Flammer, Larry


    Students compare banding patterns on hominid chromosomes and see striking evidence of their common ancestry. To test this, human chromosome no. 2 is matched with two shorter chimpanzee chromosomes, leading to the hypothesis that human chromosome 2 resulted from the fusion of the two shorter chromosomes. Students test that hypothesis by looking for…

  6. Chromosomal rearrangement interferes with meiotic X chromosome inactivation. (United States)

    Homolka, David; Ivanek, Robert; Capkova, Jana; Jansa, Petr; Forejt, Jiri


    Heterozygosity for certain mouse and human chromosomal rearrangements is characterized by the incomplete meiotic synapsis of rearranged chromosomes, by their colocalization with the XY body in primary spermatocytes, and by male-limited sterility. Previously, we argued that such X-autosomal associations could interfere with meiotic sex chromosome inactivation. Recently, supporting evidence has reported modifications of histones in rearranged chromosomes by a process called the meiotic silencing of unsynapsed chromatin (MSUC). Here, we report on the transcriptional down-regulation of genes within the unsynapsed region of the rearranged mouse chromosome 17, and on the subsequent disturbance of X chromosome inactivation. The partial transcriptional suppression of genes in the unsynapsed chromatin was most prominent prior to the mid-pachytene stage of primary spermatocytes. Later, during the mid-late pachytene, the rearranged autosomes colocalized with the XY body, and the X chromosome failed to undergo proper transcriptional silencing. Our findings provide direct evidence on the MSUC acting at the mRNA level, and implicate that autosomal asynapsis in meiosis may cause male sterility by interfering with meiotic sex chromosome inactivation.

  7. Development of a novel cell sorting method that samples population diversity in flow cytometry. (United States)

    Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L


    Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance.

  8. Magnetic cell sorting and flow cytometry sorting methods for the isolation and function analysis of mouse CD4+ CD25+ Treg cells*



    Objective: In this paper we compared the two methods of cell sorting (magnetic cell sorting and flow cytometry sorting) for the isolation and function analysis of mouse CD4+ CD25+ regulatory T (Treg) cells, in order to inform further studies in Treg cell function. Methods: We separately used magnetic cell sorting and flow cytometry sorting to identify CD4+ CD25+ Treg cells. After magnetic cell separation, we further used flow cytometry to analyze the purity of CD4+ CD25+ Treg cells, trypan bl...

  9. Structure and chromosomal localization of the gene encoding the human myelin protein zero (MPZ)

    Energy Technology Data Exchange (ETDEWEB)

    Hayasaka, Kiyoshi; Himoro, Masato; Takada, Goro (Akita Univ. School of Medicine, Akita (Japan)); Wang, Yimin; Takata, Mizuho; Minoshima, Shinsei; Shimizu, Nobuyoshi; Miura, Masayuki; Uyemura, Keiichi (Keio Univ. School of Medicine, Tokyo (Japan))


    The authors describe the cloning, characterization, and chromosomal mapping of the human myelin protein zero (MPZ) gene (a structural protein of myelin and an adhesive glycoprotein of the immunoglobulin superfamily). The gene is about 7 kb long and consists of six exons corresponding of the functional domains. All exon-intron junction sequences conform to the GT/AG rule. The 5[prime]-flanking region of the gene has a TA-rich element (TATA-like box), two CAAT boxes, and a single defined transcription initiation site detected by the primer extension method. The gene for human MPZ was assigned to chromosome 1q22-q23 by spot blot hybridization of flow-sorted human chromosomes and fluorescence in situ hybridization. The localization of the MPZ gene coincides with the locus for Charcot-Marie-Tooth disease type 1B, determined by linkage analysis. 20 refs., 3 figs., 1 tab.

  10. Parallel particle identification and separation for active optical sorting

    DEFF Research Database (Denmark)

    Perch-Nielsen, Ivan R.; Palima, Darwin; Dam, Jeppe Seidelin


    matched with a rapidly reconfigurable optical sorting field. We demonstrate the potential of such a system using colloidal polystyrene microspheres. By combining machine vision with a parallel add-on optical manipulation scheme, we were able to move identified particles over a distance of several hundred...

  11. Microbiological air quality at municipal waste sorting plant

    Directory of Open Access Journals (Sweden)

    Bulski Karol


    Full Text Available Municipal waste plants can be a source of biological contamination of the environment, depending on the method of operation and the type of collected waste. The aim of this study was the quantitative characteristics of airborne microorganisms at the Barycz municipal waste sorting plant in Cracow. Bioaerosol measurements of indoor and outdoor air of the municipal waste sorting plant were performed during the summer season using a six-stage Andersen cascade impactor. The highest concentration of bacterial and fungal aerosol was observed in the medium fraction sorting room (129.02×103 cfu·m-3 and 116.21×103 cfu·m-3, respectively. There were statistically significant differences in the concentrations of bacterial and fungal aerosol between indoor and outdoor air. The calculations showed a significant correlation between the concentration of bioaerosol and particulate matter. Based on the analysis of bioaerosol particle size distribution, it was found that the concentration of bacteria and fungi has a maximum value in the diameter range 3.3-7.0 μm. The study confirmed that the municipal waste sorting plants can be causing exposure to microbiological agents.

  12. Multiple pathways for vacuolar sorting of yeast proteinase A

    DEFF Research Database (Denmark)

    Westphal, V; Marcusson, E G; Winther, Jakob R.;


    ) overproduction of Vps10p suppressed the missorting phenotype associated with overproduction of proteinase A, 2) overproduction of proteinase A induced missorting of carboxypeptidase Y, 3) vacuolar sorting of proteinase A in a deltavps10 strain was readily saturated by modest overproduction of proteinase A, and 4...

  13. Sorting and the output loss due to search frictions

    NARCIS (Netherlands)

    P.A. Gautier; C.N. Teulings


    We analyze a general search model with on-the-job search (OJS) and sorting of heterogeneous workers into heterogeneous jobs. For given values of non-market time, the relative efciency of OJS, and the amount of search frictions, we derive a simple relationship between the unemployment rate, mismatch

  14. A methodical approach for the assessment of waste sorting plants

    NARCIS (Netherlands)

    Feil, Alexander; Pretz, Thomas; Vitz, Philipp; Thoden van Velzen, Ulphard


    A techno-economical evaluation of the processing result of waste sorting plants should at least provide a realistic assessment of the recovery yields of valuable materials and of the qualities of the obtained products. This practical data is generated by weighing all the output products and sampl

  15. Local Residential Sorting and Public Goods Provision: A Classroom Demonstration (United States)

    Brouhle, Keith; Corrigan, Jay; Croson, Rachel; Farnham, Martin; Garip, Selhan; Habodaszova, Luba; Johnson, Laurie Tipton; Johnson, Martin; Reiley, David


    This classroom exercise illustrates the Tiebout (1956) hypothesis that residential sorting across multiple jurisdictions leads to a more efficient allocation of local public goods. The exercise places students with heterogeneous preferences over a public good into a single classroom community. A simple voting mechanism determines the level of…


    NARCIS (Netherlands)



    Deficient performance on the Wisconsin Card Sorting Test (WCST) by patients with schizophrenia is a consistent finding. Although the test has been found sensitive to frontal lobe damage in neurological patients, it is not certain whether WCST performance in schizophrenia is caused by a structural ab

  17. System for sorting microscopic objects using electromagnetic radiation

    DEFF Research Database (Denmark)


    There is presented a system 10,100 for sorting microscopic objects 76, 78, 80, where the system comprises a fluid channel 66 with an inlet 68 and an outlet 70, where the fluid channel is arranged for allowing the fluid flow to be laminar. The system furthermore comprises a detection system 52 whi...

  18. Digoxin in clinical practice: sorting out the facts. (United States)

    Doi, S A; Landless, P N


    The aim of this review is to sort out from the huge amount of facts related to digoxin in the literature those pertinent to current clinical practice. Seven aspects of digoxin are discussed: its mechanism of action, therapeutic controversy, clinical efficacy, avoidance of toxicity, manifestations of toxicity, indications, and its use in coronary artery disease.

  19. Sorting Recycled Trash: An Activity for Earth Day 2007 (United States)

    Harris, Mary E.; Harris, Harold H.


    Middle or high school students celebrate Earth Day on April 22, 2007 by participating in the activity to separate commingled recyclable trash to simulate sorting in a recycling center. Students would gain an appreciation for recyclable trash, after it is taken to a recycling center and learn about properties of recyclables.

  20. Generic sorting of raft lipids into secretory vesicles in yeast

    DEFF Research Database (Denmark)

    Surma, Michal A; Klose, Christian; Klemm, Robin W;


    a complete lipid overview of the yeast late secretory pathway. We could show that vesicles captured with different baits carry the same cargo and have almost identical lipid compositions; being highly enriched in ergosterol and sphingolipids. This finding indicates that lipid raft sorting is a generic...... feature of vesicles carrying PM cargo and suggests a common lipid-based mechanism for their formation....

  1. Udpegning af potentielle sorte pletter via floating car data

    DEFF Research Database (Denmark)

    Splid Svendsen, Martin; Tradisauskas, Nerius; Lahrmann, Harry


    Formålet med dette paper er at undersøge, om det er muligt at udpege potentielle sorte pletter via floating car data. Der er i projektet udført teoretiske litteraturstudier for at skabe et grundlag for det senere analysearbejde, som danner baggrund for analysearbejdet. Dataene stammer fra Aalborg...

  2. Prediction of N-terminal protein sorting signals

    DEFF Research Database (Denmark)

    Claros, Manuel G.; Brunak, Søren; von Heijne, Gunnar


    Recently, neural networks have been applied to a widening range of problems in molecular biology. An area particularly suited to neural-network methods is the identification of protein sorting signals and the prediction of their cleavage sites, as these functional units are encoded by local, line...

  3. Tunable Superomniphobic Surfaces for Sorting Droplets by Surface Tension (United States)

    Movafaghi, Sanli; Wang, Wei; Metzger, Ari; Williams, Desiree; Williams, John; Kota, Arun


    Manipulation of liquid droplets on super-repellent surfaces (i.e., surfaces that are extremely repellent to liquids) has been widely studied because droplets exhibit high mobility on these surfaces due to the ultra-low adhesion, which leads to minimal sample loss and contamination. Although droplet manipulation has been demonstrated using electric fields, magnetic fields, guiding tracks and wettability gradients, to the best of our knowledge, there are no reports of droplet manipulation methods that can sort droplets by surface tension on super-repellent surfaces. In this work, we utilized tunable superomniphobic surfaces (i.e., surfaces that are extremely repellent to virtually all liquids) to develop a simple device with precisely tailored solid surface energy domains that, for the first time, can sort droplets by surface tension. Droplet sorting occurs on our device entirely due to a balance between the work done by gravity and the work expended due to adhesion, without the need for any external energy input. Our device can be fabricated easily in a short time and is particularly useful for in-the-field and on-the-go operations, where complex analysis equipment is unavailable. We envision that our methodology for droplet sorting will enable inexpensive and energy-efficient analytical devices for personalized point-of-care diagnostic platforms and lab-on-a-chip systems.

  4. An efficient non-dominated sorting method for evolutionary algorithms. (United States)

    Fang, Hongbing; Wang, Qian; Tu, Yi-Cheng; Horstemeyer, Mark F


    We present a new non-dominated sorting algorithm to generate the non-dominated fronts in multi-objective optimization with evolutionary algorithms, particularly the NSGA-II. The non-dominated sorting algorithm used by NSGA-II has a time complexity of O(MN(2)) in generating non-dominated fronts in one generation (iteration) for a population size N and M objective functions. Since generating non-dominated fronts takes the majority of total computational time (excluding the cost of fitness evaluations) of NSGA-II, making this algorithm faster will significantly improve the overall efficiency of NSGA-II and other genetic algorithms using non-dominated sorting. The new non-dominated sorting algorithm proposed in this study reduces the number of redundant comparisons existing in the algorithm of NSGA-II by recording the dominance information among solutions from their first comparisons. By utilizing a new data structure called the dominance tree and the divide-and-conquer mechanism, the new algorithm is faster than NSGA-II for different numbers of objective functions. Although the number of solution comparisons by the proposed algorithm is close to that of NSGA-II when the number of objectives becomes large, the total computational time shows that the proposed algorithm still has better efficiency because of the adoption of the dominance tree structure and the divide-and-conquer mechanism.

  5. Effektive ledergrupper eller sorte huller fra top til front

    DEFF Research Database (Denmark)

    Elmholdt, Claus Westergård; Molly-Søholm, Thorkil


    Effektive ledergrupper Ledergrupper er centrum for organisationers struktur og praksis, men ledergrupper kan også udvikle sig til ’sorte huller’, som driver al energi, effektivitet og trivsel ud af ikke bare den enkelte leder, men ud af hele organisationen. En ny undersøgelse blandt 76 danske led...

  6. Parallel sort with a ranged, partitioned key-value store in a high perfomance computing environment (United States)

    Bent, John M.; Faibish, Sorin; Grider, Gary; Torres, Aaron; Poole, Stephen W.


    Improved sorting techniques are provided that perform a parallel sort using a ranged, partitioned key-value store in a high performance computing (HPC) environment. A plurality of input data files comprising unsorted key-value data in a partitioned key-value store are sorted. The partitioned key-value store comprises a range server for each of a plurality of ranges. Each input data file has an associated reader thread. Each reader thread reads the unsorted key-value data in the corresponding input data file and performs a local sort of the unsorted key-value data to generate sorted key-value data. A plurality of sorted, ranged subsets of each of the sorted key-value data are generated based on the plurality of ranges. Each sorted, ranged subset corresponds to a given one of the ranges and is provided to one of the range servers corresponding to the range of the sorted, ranged subset. Each range server sorts the received sorted, ranged subsets and provides a sorted range. A plurality of the sorted ranges are concatenated to obtain a globally sorted result.

  7. Cohesin in determining chromosome architecture

    Energy Technology Data Exchange (ETDEWEB)

    Haering, Christian H., E-mail: [Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg (Germany); Jessberger, Rolf, E-mail: [Institute of Physiological Chemistry, Dresden University of Technology, Dresden (Germany)


    Cells use ring-like structured protein complexes for various tasks in DNA dynamics. The tripartite cohesin ring is particularly suited to determine chromosome architecture, for it is large and dynamic, may acquire different forms, and is involved in several distinct nuclear processes. This review focuses on cohesin's role in structuring chromosomes during mitotic and meiotic cell divisions and during interphase.

  8. Waste Sorting Habits by the Community of Kaunas University of Technology, Reasons and Influencing Factors

    Directory of Open Access Journals (Sweden)

    Toma Adomavičiūtė


    Full Text Available The article presents the waste management system at Kaunas University of Technology, surveys the waste sorting habits of its community, both students and employees, and analyses the reasons and factors influencing waste sorting and non-sorting. The introduction of a separate paper waste collection system has made it possible to reduce the amount of mixed waste by 25% during the first three months of its functioning. 58% of employees and 45% of students sort some of their waste partly, 23% of employees and 11% of students sort all their waste. 8% of employees and 19% of students sort their waste sometimes. 8% of employees and 24% of students do not sort waste at all. 77% of employees and 66% of students think that the main problem caused by waste generation is pollution of the environment. Therefore willingness to reduce an impact on it is the main reason for sorting, while a lack of conditions to keep separated recyclable refuse and a lack of nearby containers are main factors that are distracting people from source-sorting. Growth of environmental awareness and formation of sorting habits that are transmitted to family members are identified as the strengths. Lack of conditions for sorting (e.g. no place to keep sorted waste at home, insufficiently developed waste collection infrastructure, mistrust in a sorted waste collection system (e.g. belief that sorted waste goes to a landfill, and lack of information are the weaknesses. The opportunities comprise development of a convenient waste collection infrastructure, introduction of economic incentives and rise of further awareness. Identified threats for sorting at the source that discourage source sorting are the following: a developed infrastructure will not satisfy real needs; sorting will not become financially rewarding; improper decisions about a waste management system and waste treatment practices made at the state level, no real use of sorting.DOI:

  9. Genetics Home Reference: Y chromosome infertility (United States)

    ... Home Health Conditions Y chromosome infertility Y chromosome infertility Enable Javascript to view the expand/collapse boxes. ... PDF Open All Close All Description Y chromosome infertility is a condition that affects the production of ...

  10. Higher order structure of chromosomes. (United States)

    Okada, T A; Comings, D E


    Isolated Chinese hamster metaphase chromosomes were resuspended in 4 M ammonium acetate and spread on a surface of distilled water or 0.15 to 0.5 M ammonium acetate. The DNA was released in the form of a regular series of rosettes connected by interrossette DNA. The mean length of the rosette DNA was 14 micron, similar to the mean length of 10 micron for chromomere DNA of Drosophila polytene chromosomes. The mean interrosette DNA was 4.2 micron. SDS gel electrophoresis of the chromosomal nonhistone proteins showed them to be very similar to nuclear nonhistone proteins except for the presence of more actin and tubulin. Nuclear matrix proteins were present in the chromosomes and may play a role in forming the rosettes. Evidence that the rosette pattern is artifactual versus the possibility that it represents a real organizational substructure of the chromosomes is reviewed.

  11. Bacterial chromosome organization and segregation. (United States)

    Badrinarayanan, Anjana; Le, Tung B K; Laub, Michael T


    If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.

  12. Chromosome choreography: the meiotic ballet. (United States)

    Page, Scott L; Hawley, R Scott


    The separation of homologous chromosomes during meiosis in eukaryotes is the physical basis of Mendelian inheritance. The core of the meiotic process is a specialized nuclear division (meiosis I) in which homologs pair with each other, recombine, and then segregate from each other. The processes of chromosome alignment and pairing allow for homolog recognition. Reciprocal meiotic recombination ensures meiotic chromosome segregation by converting sister chromatid cohesion into mechanisms that hold homologous chromosomes together. Finally, the ability of sister kinetochores to orient to a single pole at metaphase I allows the separation of homologs to two different daughter cells. Failures to properly accomplish this elegant chromosome dance result in aneuploidy, a major cause of miscarriage and birth defects in human beings.

  13. Schizophrenia and chromosomal deletions

    Energy Technology Data Exchange (ETDEWEB)

    Lindsay, E.A.; Baldini, A. [Baylor College of Medicine, Houston, TX (United States); Morris, M. A. [Univ. of Geneva School of Medicine, NY (United States)] [and others


    Recent genetic linkage analysis studies have suggested the presence of a schizophrenia locus on the chromosomal region 22q11-q13. Schizophrenia has also been frequently observed in patients affected with velo-cardio-facial syndrome (VCFS), a disorder frequently associated with deletions within 22q11.1. It has been hypothesized that psychosis in VCFS may be due to deletion of the catechol-o-methyl transferase gene. Prompted by these observations, we screened for 22q11 deletions in a population of 100 schizophrenics selected from the Maryland Epidemiological Sample. Our results show that there are schizophrenic patients carrying a deletion of 22q11.1 and a mild VCFS phenotype that might remain unrecognized. These findings should encourage a search for a schizophrenia-susceptibility gene within the deleted region and alert those in clinical practice to the possible presence of a mild VCFS phenotype associated with schizophrenia. 9 refs.

  14. Chromatid Painting for Chromosomal Inversion Detection Project (United States)

    National Aeronautics and Space Administration — We propose the continued development of a novel approach to the detection of chromosomal inversions. Transmissible chromosome aberrations (translocations and...



  16. Chromatid Painting for Chromosomal Inversion Detection Project (United States)

    National Aeronautics and Space Administration — We propose a novel approach to the detection of chromosomal inversions. Transmissible chromosome aberrations (translocations and inversions) have profound genetic...

  17. Development of a two-parameter slit-scan flow cytometer for screening of normal and aberrant chromosomes: application to a karyotype of Sus scrofa domestica (pig) (United States)

    Hausmann, Michael; Doelle, Juergen; Arnold, Armin; Stepanow, Boris; Wickert, Burkhard; Boscher, Jeannine; Popescu, Paul C.; Cremer, Christoph


    Laser fluorescence activated slit-scan flow cytometry offers an approach to a fast, quantitative characterization of chromosomes due to morphological features. It can be applied for screening of chromosomal abnormalities. We give a preliminary report on the development of the Heidelberg slit-scan flow cytometer. Time-resolved measurement of the fluorescence intensity along the chromosome axis can be registered simultaneously for two parameters when the chromosome axis can be registered simultaneously for two parameters when the chromosome passes perpendicularly through a narrowly focused laser beam combined by a detection slit in the image plane. So far automated data analysis has been performed off-line on a PC. In its final performance, the Heidelberg slit-scan flow cytometer will achieve on-line data analysis that allows an electro-acoustical sorting of chromosomes of interest. Interest is high in the agriculture field to study chromosome aberrations that influence the size of litters in pig (Sus scrofa domestica) breeding. Slit-scan measurements have been performed to characterize chromosomes of pigs; we present results for chromosome 1 and a translocation chromosome 6/15.

  18. Mitotic chromosome condensation in vertebrates

    Energy Technology Data Exchange (ETDEWEB)

    Vagnarelli, Paola, E-mail:


    Work from several laboratories over the past 10-15 years has revealed that, within the interphase nucleus, chromosomes are organized into spatially distinct territories [T. Cremer, C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells, Nat. Rev. Genet. 2 (2001) 292-301 and T. Cremer, M. Cremer, S. Dietzel, S. Muller, I. Solovei, S. Fakan, Chromosome territories-a functional nuclear landscape, Curr. Opin. Cell Biol. 18 (2006) 307-316]. The overall compaction level and intranuclear location varies as a function of gene density for both entire chromosomes [J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague,W.A. Bickmore, Differences in the localization and morphology of chromosomes in the human nucleus, J. Cell Biol. 145 (1999) 1119-1131] and specific chromosomal regions [N.L. Mahy, P.E. Perry, S. Gilchrist, R.A. Baldock, W.A. Bickmore, Spatial organization of active and inactive genes and noncoding DNA within chromosome territories, J. Cell Biol. 157 (2002) 579-589] (Fig. 1A, A'). In prophase, when cyclin B activity reaches a high threshold, chromosome condensation occurs followed by Nuclear Envelope Breakdown (NEB) [1]. At this point vertebrate chromosomes appear as compact structures harboring an attachment point for the spindle microtubules physically recognizable as a primary constriction where the two sister chromatids are held together. The transition from an unshaped interphase chromosome to the highly structured mitotic chromosome (compare Figs. 1A and B) has fascinated researchers for several decades now; however a definite picture of how this process is achieved and regulated is not yet in our hands and it will require more investigation to comprehend the complete process. From a biochemical point of view a vertebrate mitotic chromosomes is composed of DNA, histone proteins (60%) and non-histone proteins (40%) [6]. I will discuss below what is known to date on the contribution of these two different classes

  19. Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

    Directory of Open Access Journals (Sweden)

    Doležel Jaroslav


    Full Text Available Abstract Background The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy. Results The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the

  20. Buoyancy-activated cell sorting using targeted biotinylated albumin microbubbles.

    Directory of Open Access Journals (Sweden)

    Yu-Ren Liou

    Full Text Available Cell analysis often requires the isolation of certain cell types. Various isolation methods have been applied to cell sorting, including fluorescence-activated cell sorting and magnetic-activated cell sorting. However, these conventional approaches involve exerting mechanical forces on the cells, thus risking cell damage. In this study we applied a novel isolation method called buoyancy-activated cell sorting, which involves using biotinylated albumin microbubbles (biotin-MBs conjugated with antibodies (i.e., targeted biotin-MBs. Albumin MBs are widely used as contrast agents in ultrasound imaging due to their good biocompatibility and stability. For conjugating antibodies, biotin is conjugated onto the albumin MB shell via covalent bonds and the biotinylated antibodies are conjugated using an avidin-biotin system. The albumin microbubbles had a mean diameter of 2 μm with a polydispersity index of 0.16. For cell separation, the MDA-MB-231 cells are incubated with the targeted biotin-MBs conjugated with anti-CD44 for 10 min, centrifuged at 10 g for 1 min, and then allowed 1 hour at 4 °C for separation. The results indicate that targeted biotin-MBs conjugated with anti-CD44 antibodies can be used to separate MDA-MB-231 breast cancer cells; more than 90% of the cells were collected in the MB layer when the ratio of the MBs to cells was higher than 70:1. Furthermore, we found that the separating efficiency was higher for targeted biotin-MBs than for targeted avidin-incorporated albumin MBs (avidin-MBs, which is the most common way to make targeted albumin MBs. We also demonstrated that the recovery rate of targeted biotin-MBs was up to 88% and the sorting purity was higher than 84% for a a heterogenous cell population containing MDA-MB-231 cells (CD44(+ and MDA-MB-453 cells (CD44-, which are classified as basal-like breast cancer cells and luminal breast cancer cells, respectively. Knowing that the CD44(+ is a commonly used cancer

  1. The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds.

    Directory of Open Access Journals (Sweden)

    Alexander Suh


    Full Text Available The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS, i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

  2. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes. (United States)

    Thierry, A; Dujon, B


    We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.

  3. Gametocidal chromosomes enhancing chromosome aberration in common wheat induced by 5-azacytidine. (United States)

    Su, W-Y; Cong, W-W; Shu, Y-J; Wang, D; Xu, G-H; Guo, C-H


    The gametocidal (Gc) chromosome from Aegilops spp induces chromosome mutation, which is introduced into common wheat as a tool of chromosome manipulation for genetic improvement. The Gc chromosome functions similar to a restriction-modification system in bacteria, in which DNA methylation is an important regulator. We treated root tips of wheat carrying Gc chromosomes with the hypomethylation agent 5-azacytidine; chromosome breakage and micronuclei were observed in these root tips. The frequency of aberrations differed in wheat containing different Gc chromosomes, suggesting different functions inducing chromosome breakage. Gc chromosome 3C caused the greatest degree of chromosome aberration, while Gc chromosome 3C(SAT) and 2C caused only slight chromosome aberration. Gc chromosome 3C induced different degrees of chromosome aberration in wheat varieties Triticum aestivum var. Chinese Spring and Norin 26, demonstrating an inhibition function in common wheat.

  4. Chromosome segregation in Vibrio cholerae. (United States)

    Ramachandran, Revathy; Jha, Jyoti; Chattoraj, Dhruba K


    The study of chromosome segregation is currently one of the most exciting research frontiers in cell biology. In this review, we discuss our current knowledge of the chromosome segregation process in Vibrio cholerae, based primarily on findings from fluorescence microscopy experiments. This bacterium is of special interest because of its eukaryotic feature of having a divided genome, a feature shared with 10% of known bacteria. We also discuss how the segregation mechanisms of V. cholerae compare with those in other bacteria, and highlight some of the remaining questions regarding the process of bacterial chromosome segregation.

  5. Numerous transitions of sex chromosomes in Diptera. (United States)

    Vicoso, Beatriz; Bachtrog, Doris


    Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.

  6. Design of monitoring system for mail-sorting based on the Profibus S7 series PLC (United States)

    Zhang, W.; Jia, S. H.; Wang, Y. H.; Liu, H.; Tang, G. C.


    With the rapid development of the postal express, the workload of mail sorting is increasing, but the automatic technology of mail sorting is not mature enough. In view of this, the system uses Siemens S7-300 PLC as the main station controller, PLC of Siemens S7-200/400 is from the station controller, through the man-machine interface configuration software MCGS, PROFIBUS-DP communication, RFID technology and mechanical sorting hand achieve mail classification sorting monitoring. Among them, distinguish mail-sorting by scanning RFID posted in the mail electronic bar code (fixed code), the system uses the corresponding controller on the acquisition of information processing, the processed information transmit to the sorting manipulator by PROFIBUS-DP. The system can realize accurate and efficient mail sorting, which will promote the development of mail sorting technology.

  7. Constant-time parallel sorting algorithm and its optical implementation using smart pixels (United States)

    Louri, Ahmed; Hatch, James A., Jr.; Na, Jongwhoa


    Sorting is a fundamental operation that has important implications in a vast number of areas. For instance, sorting is heavily utilized in applications such as database machines, in which hashing techniques are used to accelerate data-processing algorithms. It is also the basis for interprocessor message routing and has strong implications in video telecommunications. However, high-speed electronic sorting networks are difficult to implement with VLSI technology because of the dense, global connectivity required. Optics eliminates this bottleneck by offering global interconnects, massive parallelism, and noninterfering communications. We present a parallel sorting algorithm and its efficient optical implementation. The algorithm sorts n data elements in few steps, independent of the number of elements to be sorted. Thus it is a constant-time sorting algorithm [i.e., O(1) time]. We also estimate the system's performance to show that the proposed sorting algorithm can provide at least 2 orders of magnitude improvement in execution time over conventional electronic algorithms.

  8. A Comparative Analysis of Deterministic Sorting Algorithms based on Runtime and Count of Various Operations

    Directory of Open Access Journals (Sweden)

    Reyha Verma


    Full Text Available Sorting algorithms find its application in many practical fields of Computer Science. Efficient solving of sorting problem has attracted a great deal of research as it optimizes other algorithms also. The main factor which is taken into consideration while determining the efficiency of a sorting algorithm is the time complexity. Mostly the execution time of algorithms is investigated and compared for analyzing time complexity. This paper presents a comparative analysis of deterministic sorting algorithms. Time complexity of six different algorithms namely, Selection sort, Bubble sort, Insertion sort, Quicksort, Heapsort and Mergesort is determined in terms of number of comparisons, swaps and assignment operations in addition to average execution time. Also, the performance of these algorithms on fully and almost sorted lists was also analyzed. The study indicates that determining the operation’s count is essential for analyzing time complexity especially when algorithms are theoretically analyzed.

  9. An Empirical Model of Wage Dispersion with Sorting

    DEFF Research Database (Denmark)

    Bagger, Jesper; Lentz, Rasmus

    This paper studies wage dispersion in an equilibrium on-the-job-search model with endogenous search intensity. Workers differ in their permanent skill level and firms differ with respect to productivity. Positive (negative) sorting results if the match production function is supermodular (submodu......This paper studies wage dispersion in an equilibrium on-the-job-search model with endogenous search intensity. Workers differ in their permanent skill level and firms differ with respect to productivity. Positive (negative) sorting results if the match production function is supermodular...... (submodular). The model is estimated on Danish matched employer-employee data. We find evidence of positive assortative matching. In the estimated equilibrium match distribution, the correlation between worker skill and firm productivity is 0.12. The assortative matching has a substantial impact on wage...

  10. Particle sorting using a porous membrane in a microfluidic device. (United States)

    Wei, Huibin; Chueh, Bor-han; Wu, Huiling; Hall, Eric W; Li, Cheuk-wing; Schirhagl, Romana; Lin, Jin-Ming; Zare, Richard N


    Porous membranes have been fabricated based on the development of the perforated membrane mold [Y. Luo and R. N. Zare, Lab Chip, 2008, 8, 1688-1694] to create a single filter that contains multiple pore sizes ranging from 6.4 to 16.6 µm inside a monolithic three-dimensional poly(dimethylsiloxane) microfluidic structure. By overlapping two filters we are able to achieve smaller pore size openings (2.5 to 3.3 µm). This filter operates without any detectable irreversible clogging, which is achieved using a cross-flow placed in front of each filtration section. The utility of a particle-sorting device that contains this filter is demonstrated by separating polystyrene beads of different diameters with an efficiency greater than 99.9%. Additionally, we demonstrate the effectiveness of this particle-sorting device by separating whole blood samples into white blood cells and red blood cells with platelets.

  11. Armoring and vertical sorting in aeolian dune fields (United States)

    Gao, Xin; Narteau, Clément; Rozier, Olivier


    Unlike ripples, there are only few numerical studies on grain-size segregation at the scale of dunes in aeolian environments. Here we use a cellular automaton model to analyze vertical sorting in granular mixtures under steady unidirectional flow conditions. We investigate the feedbacks between dune growth and the segregation mechanisms by varying the size of coarse grains and their proportion within the bed. We systematically observe the development of a horizontal layer of coarse grains at the top of which sorted bed forms may grow by amalgamation. The formation of such an armor layer controls the overall sediment transport and availability. The emergence of dunes and the transition from barchan to transverse dune fields depend only on the grain size distribution of the initial sediment layer. As confirmed by observation, this result indicates that armor layers should be present in most arid deserts, where they are likely to control dune morphodynamics.

  12. Neural Network Based Color Recognition for Bobbin Sorting Machine

    Directory of Open Access Journals (Sweden)

    Mu Zhang


    Full Text Available Winding is a key process in the manufacturing process of textile industry. The normal and effective operation of winding process plays a very important role on the textiles’ quality and economic effects. At present, a large proportion of bobbins which collected from winder still have yarn left over. The bobbin recycling is severely limited and quick running of winder is seriously restricted, the invention of the the automatic bobbin sorting machine has solved this problem. The ability to distinguish bobbin which has yarn left over from the rest and the classification accuracy of color are the two important performance indicators for bobbin sorting machine. According to the development and application of the color recognition technology and the artificial intelligence method, this study proposes a novel color recognition method that based on BP neural networks. The result shows that the accuracy of color recognition reaches 98%.  

  13. Gallium Nitride Electrical Characteristics Extraction and Uniformity Sorting

    Directory of Open Access Journals (Sweden)

    Shyr-Long Jeng


    Full Text Available This study examined the output electrical characteristics—current-voltage (I-V output, threshold voltage, and parasitic capacitance—of novel gallium nitride (GaN power transistors. Experimental measurements revealed that both enhanced- and depletion-mode GaN field-effect transistors (FETs containing different components of identical specifications yielded varied turn-off impedance; hence, the FET quality was inconsistent. Establishing standardized electrical measurements can provide necessary information for designers, and measuring transistor electrical characteristics establishes its equivalent-circuit model for circuit simulations. Moreover, high power output requires multiple parallel power transistors, and sorting the difference between similar electrical characteristics is critical in a power system. An isolated gate driver detection method is proposed for sorting the uniformity from the option of the turn-off characteristic. In addition, an equivalent-circuit model for GaN FETs is established on the basis of the measured electrical characteristics and verified experimentally.

  14. What about inhibition in the Wisconsin Card Sorting Test? (United States)

    Steinmetz, Jean-Paul; Houssemand, Claude


    The commercially available Wisconsin Card Sorting Test (WCST) is one of the most commonly used tests for assessing executive functions within clinical settings. Importantly, however, it remains relatively unclear exactly what processes are assessed by the test. Conceptually, increased perseverative errors in sorting cards are usually related to deficient inhibition processes. Empirically, evidence supporting this conclusion is limited. In a sample of 38 healthy adults we addressed the question to what extent inhibition mechanisms assessed by the go/no-go and the stop-signal paradigm are related to WCST performances. Inhibition-related scores were found to predict non-perseverative errors better than perseverative errors. Consequently we conclude that the non-perseverative errors score reflects processes that are partly dependent on inhibition functions.

  15. Control of a brain-computer interface without spike sorting (United States)

    Fraser, George W.; Chase, Steven M.; Whitford, Andrew; Schwartz, Andrew B.


    Two rhesus monkeys were trained to move a cursor using neural activity recorded with silicon arrays of 96 microelectrodes implanted in the primary motor cortex. We have developed a method to extract movement information from the recorded single and multi-unit activity in the absence of spike sorting. By setting a single threshold across all channels and fitting the resultant events with a spline tuning function, a control signal was extracted from this population using a Bayesian particle-filter extraction algorithm. The animals achieved high-quality control comparable to the performance of decoding schemes based on sorted spikes. Our results suggest that even the simplest signal processing is sufficient for high-quality neuroprosthetic control.

  16. Improved Sorting-Based Procedure for Integer Programming

    DEFF Research Database (Denmark)

    Dantchev, Stefan


    Recently, Cornuéjols and Dawande have considered a special class of 0-1 programs that turns out to be hard for existing IP solvers. One of them is a sorting-based algorithm, based on an idea of Wolsey. In this paper, we show how to improve both the running time and the space requirements of this ......Recently, Cornuéjols and Dawande have considered a special class of 0-1 programs that turns out to be hard for existing IP solvers. One of them is a sorting-based algorithm, based on an idea of Wolsey. In this paper, we show how to improve both the running time and the space requirements...... of this algorithm. The drastic reduction of space needed allows us to solve much larger instances than was possible before using this technique....

  17. Constructing Efficient Dictionaries in Close to Sorting Time

    DEFF Research Database (Denmark)

    Ruzic, Milan


    -case cost of construction of the structures is proportional to only loglogn times the cost of sorting the input. Our claimed performance bounds are obtained in the word RAM model and in the external memory models; only the involved sorting procedures in the algorithms need to be changed between the models.......The dictionary problem is among the oldest problems in computer science. Yet our understanding of the complexity of the dictionary problem in realistic models of computation has been far from complete. Designing highly efficient dictionaries without resorting to use of randomness appeared...... to be a particularly challenging task. We present solutions to the static dictionary problem that significantly improve the previously known upper bounds and bring them close to obvious lower bounds. Our dictionaries have a constant lookup cost and use linear space, which was known to be possible, but the worst...

  18. Large area magnetic micropallet arrays for cell colony sorting. (United States)

    Cox-Muranami, Wesley A; Nelson, Edward L; Li, G P; Bachman, Mark


    A new micropallet array platform for adherent cell colony sorting has been developed. The platform consisted of thousands of square plastic pallets, 270 μm by 270 μm on each side, large enough to hold a single colony of cells. Each pallet included a magnetic core, allowing them to be collected with a magnet after being released using a microscope mounted laser system. The micropallets were patterned from 1002F epoxy resist and were fabricated on translucent, gold coated microscope slides. The gold layer was used as seed for electroplating the ferromagnetic cores within every individual pallet. The gold layer also facilitated the release of each micropallet during laser release. This array allows for individual observation, sorting and collection of isolated cell colonies for biological cell colony research. In addition to consistent release and recovery of individual colonies, we demonstrated stable biocompatibility and minimal loss in imaging quality compared to previously developed micropallet arrays.

  19. Sorting and Manipulation of Magnetic Droplets in Continuous Flow (United States)

    Al-Hetlani, Entesar; Hatt, Oliver J.; Vojtíšek, Martin; Tarn, Mark D.; Iles, Alexander; Pamme, Nicole


    We report the rapid on-chip generation and subsequent manipulation of magnetic droplets in continuous flow. Magnetic droplets were formed using aqueous-based ferrofluid as the dispersed phase and fluorocarbon oil as the continuous phase. Droplet manipulation was demonstrated with simple permanent magnets using two microfluidic platforms: (i) flow focusing droplet generation followed by their splitting into daughter droplets containing different amounts of magnetic nanoparticles, and (ii) droplet generation at a T-junction and their downstream deflection across a chamber for sorting based on the applied magnetic field and magnetite loading of the droplet. Both systems show great potential for performing a wide range of high throughput continuous flow processes including sample dilution, cell sorting and screening, and microparticle fabrication.

  20. Automatic sorting of point pattern sets using Minkowski Functionals

    CERN Document Server

    Parker, Joshua; van de Raa, Matthias; van der Meer, Devaraj; Samelson, Lawrence E; Losert, Wolfgang


    Point pattern sets arise in many different areas of physical, biological, and applied research, representing many random realizations of underlying pattern formation mechanisms. These pattern sets can be heterogeneous with respect to underlying spatial processes, which may not be visually distinguishable. This heterogeneity can be elucidated by looking at statistical measures of the patterns sets and using these measures to divide the pattern set into distinct groups representing like spatial processes. We introduce here a numerical procedure for sorting point pattern sets into spatially homogeneous groups using Functional Principal Component Analysis (FPCA) applied to the approximated Minkowski functionals of each pattern. We demonstrate that this procedure correctly sorts pattern sets into similar groups both when the patterns are drawn from similar processes and when the 2nd-order characteristics of the pattern are identical. We highlight this routine for distinguishing the molecular patterning of fluoresc...

  1. Physiology and Pathology of Endosome-to-Golgi Retrograde Sorting


    Burd, Christopher G.


    Bi-directional traffic between the Golgi apparatus and the endosomal system sustains the functions of the trans Golgi network (TGN) in secretion and organelle biogenesis. Export of cargo from the TGN via the anterograde pathways depletes the organelle of sorting receptors, processing proteases, SNARE molecules, and other factors that are subsequently retrieved from endosomes via the retrograde pathway. Recent studies indicate that retrograde trafficking is vital to early metazoan development,...

  2. Parallel Sorted Neighborhood Blocking with MapReduce


    Kolb, Lars; Thor, Andreas; Rahm, Erhard


    Cloud infrastructures enable the efficient parallel execution of data-intensive tasks such as entity resolution on large datasets. We investigate challenges and possible solutions of using the MapReduce programming model for parallel entity resolution. In particular, we propose and evaluate two MapReduce-based implementations for Sorted Neighborhood blocking that either use multiple MapReduce jobs or apply a tailored data replication.

  3. Sorting, Searching, and Simulation in the MapReduce Framework

    DEFF Research Database (Denmark)

    Goodrich, Michael T.; Sitchinava, Nodar; Zhang, Qin


    We study the MapReduce framework from an algorithmic standpoint, providing a generalization of the previous algorithmic models for MapReduce. We present optimal solutions for the fundamental problems of all-prefix-sums, sorting and multi-searching. Additionally, we design optimal simulations...... of the the well-established PRAM and BSP models in MapReduce, immediately resulting in optimal solutions to the problems of computing fixed-dimensional linear programming and 2-D and 3-D convex hulls....

  4. Two-sorted Point-Interval Temporal Logics

    DEFF Research Database (Denmark)

    Balbiani, Philippe; Goranko, Valentin; Sciavicco, Guido


    There are two natural and well-studied approaches to temporal ontology and reasoning: point-based and interval-based. Usually, interval-based temporal reasoning deals with points as particular, duration-less intervals. Here we develop explicitly two-sorted point-interval temporal logical framework...... their expressiveness, comparative to interval-based logics, and the complexity of their satisfiability problems. In particular, we identify some previously not studied and potentially interesting interval logics. © 2011 Elsevier B.V....

  5. Sorting Through Affirmative Action: Two Field Experiments in Colombia



    Affirmative action is a subject of intense debate. Supporters point to the increased representation of women and minority groups while critics contend that affirmative action can lead to inefficiencies. In this paper we present results from two field experiments that were designed to test how applicants sort in response to affirmative action rules that favor of women. Our results suggest that the criticism of affirmative action is misplaced. We find that affirmative action does not lead to lo...

  6. Sorting on Skills and Preferences: Tinbergen Meets Sattinger


    Dupuy, A.


    This paper proposes an assignment model where sorting occurs on attributes that are simultaneously a skill (Sattinger, 1979) and a preference (Tinbergen, 1956). The key feature of this model is that the wage function admits both jobs'' and workers'' attributes as arguments. Since this function is generically nonlinear (Ekeland et al., 2004), even under positive assortative matching, the correlation between the contribution of workers'' attributes to wages and that of jobs'' attributes can var...


    Directory of Open Access Journals (Sweden)

    Jana Halčinová


    Full Text Available The aim of the present article is to show the possibility of using the methods of cluster analysis in classification of stocks of finished products. Cluster analysis creates groups (clusters of finished products according to similarity in demand i.e. customer requirements for each product. Manner stocks sorting of finished products by clusters is described a practical example. The resultants clusters are incorporated into the draft layout of the distribution warehouse.

  8. Incomplete Lineage Sorting: Consistent Phylogeny Estimation From Multiple Loci

    CERN Document Server

    Mossel, Elchanan


    We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our technique is statistically consistent under standard stochastic assumptions, that is, it returns the correct tree given sufficiently many unlinked loci. We also show that it can tolerate moderate estimation errors.

  9. The Generation of a Sort of Fractal Graphs

    Institute of Scientific and Technical Information of China (English)

    张钹; 张铃; 等


    We present an approach for generating a sort of fractal graphs by a simple probabilistic logic neuron network and show that the graphs can be represented by a set of compressed codings.An algorithm for quickly finding the codings,i.e.,recognizing the corresponding graphs,is given.The codings are shown to be optimal.The results above possibly give us the clue for studying image compression and pattern recognition.

  10. Selective sorting of waste - not much effort needed, just willpower

    CERN Multimedia


    In order to keep as low as possible the cost of disposing of waste materials, CERN provides in the entrance to each building two types of recipient: a green plastic one for paper/cardboard and a metallic one for general refuse. For some time now, we have noticed, to our great regret, a growing neglect as far as the selective sorting is concerned, for example the green recipients being filled with a mixture of cardboard boxes full of polystyrene or of protective wrappers, plastic bottles, empty yogurts pots, etc …We have been able to ascertain, after carefully checking, that this haphazard mixing of waste cannot be attributed to the cleaning staff but rather to members of personnel who unscrupulously throw away their rubbish in a completely random manner. Waste non sorted entails heavy costs for CERN. For your information, once a non-compliant item is found in a green recipient, the entire contents are sent off for incineration rather than recycling… We are all concerned by selective sorting of waste mater...

  11. Association Sorting Algorithm Design for Error Searching System (United States)

    Yang, Fan; Dong, Zhenghong; Li, Mengwei


    For the searching results of error searching system for Integrated Decision Information System (IDIS), this paper proposed a method to carry out association sorting according to degree of association of searched results by keywords, which can priorily recommend user interested searching results. Errors of IDIS platform are occurred very often. Because those errors belong to different stages like setup, configuration, and operation, or those errors may occurred in different services, applications, or IP ports, or may be happened in different system software, different version of software, and those errors are also can be classified into different types. As there will be many error information are searched out, it is required to sort them according to degree of association, and provide user interested results. This paper proposed a method to carry out association sorting for the searching results according to the times of searched repeated results by keywords, which effectively put results with high degree of association in the front and increase the searching efficiency.

  12. Efficient Architecture for Spike Sorting in Reconfigurable Hardware

    Directory of Open Access Journals (Sweden)

    Sheng-Ying Lai


    Full Text Available This paper presents a novel hardware architecture for fast spike sorting. The architecture is able to perform both the feature extraction and clustering in hardware. The generalized Hebbian algorithm (GHA and fuzzy C-means (FCM algorithm are used for feature extraction and clustering, respectively. The employment of GHA allows efficient computation of principal components for subsequent clustering operations. The FCM is able to achieve near optimal clustering for spike sorting. Its performance is insensitive to the selection of initial cluster centers. The hardware implementations of GHA and FCM feature low area costs and high throughput. In the GHA architecture, the computation of different weight vectors share the same circuit for lowering the area costs. Moreover, in the FCM hardware implementation, the usual iterative operations for updating the membership matrix and cluster centroid are merged into one single updating process to evade the large storage requirement. To show the effectiveness of the circuit, the proposed architecture is physically implemented by field programmable gate array (FPGA. It is embedded in a System-on-Chip (SOC platform for performance measurement. Experimental results show that the proposed architecture is an efficient spike sorting design for attaining high classification correct rate and high speed computation.

  13. Aqueous Self-Sorting in Extended Supramolecular Aggregates

    Directory of Open Access Journals (Sweden)

    Gustavo Fernández


    Full Text Available Self-organization and self-sorting processes are responsible for the regulation and control of the vast majority of biological processes that eventually sustain life on our planet. Attempts to unveil the complexity of these systems have been devoted to the investigation of the binding processes between artificial molecules, complexes or aggregates within multicomponent mixtures, which has facilitated the emergence of the field of self-sorting in the last decade. Since, artificial systems involving discrete supramolecular structures, extended supramolecular aggregates or gel-phase materials in organic solvents or—to a lesser extent—in water have been investigated. In this review, we have collected diverse strategies employed in recent years to construct extended supramolecular aggregates in water upon self-sorting of small synthetic molecules. We have made particular emphasis on co-assembly processes in binary mixtures leading to supramolecular structures of remarkable complexity and the influence of different external variables such as solvent and concentration to direct recognition or discrimination processes between these species. The comprehension of such recognition phenomena will be crucial for the organization and evolution of complex matter.

  14. Structural determinants allowing endolysosomal sorting and degradation of endosomal GTPases. (United States)

    Valero, Ruth A; Oeste, Clara L; Stamatakis, Konstantinos; Ramos, Irene; Herrera, Mónica; Boya, Patricia; Pérez-Sala, Dolores


    Rapid control of protein degradation is usually achieved through the ubiquitin-proteasome pathway. We recently found that the short-lived GTPase RhoB is degraded in lysosomes. Moreover, the fusion of the RhoB C-terminal sequence CINCCKVL, containing the isoprenylation and palmitoylation sites, to other proteins directs their sorting into multivesicular bodies (MVBs) and rapid lysosomal degradation. Here, we show that this process is highly specific for RhoB. Alteration of late endosome lipid dynamics produced the accumulation of RhoB, but not of other endosomal GTPases, including Rab5, Rab7, Rab9 or Rab11, into enlarged MVB. Other isoprenylated and bipalmitoylated GTPases, such as H-Ras, Rap2A, Rap2B and TC10, were not accumulated into MVB and were stable. Remarkably, although TC10, which is highly homologous to RhoB, was stable, a sequence derived from its C-terminus (CINCCLIT) elicited MVB sorting and degradation of a green fluorescent protein (GFP)-chimeric protein. This led us to identify a cluster of basic amino acids (KKH) in the TC10 hypervariable region, constituting a secondary signal potentially involved in electrostatic interactions with membrane lipids. Mutation of this cluster allowed TC10 MVB sorting and degradation, whereas inserting it into RhoB hypervariable region rescued this protein from its lysosomal degradation pathway. These findings define a highly specific structural module for entering the MVB pathway and rapid lysosomal degradation.

  15. Exosome and Exosomal MicroRNA:Trafficking, Sorting, and Function

    Institute of Scientific and Technical Information of China (English)

    Jian Zhang; Sha Li; Lu Li; Meng Li; Chongye Guo; Jun Yao; Shuangli Mi


    Exosomes are 40–100 nm nano-sized vesicles that are released from many cell types into the extracellular space. Such vesicles are widely distributed in various body fluids. Recently, mRNAs and microRNAs (miRNAs) have been identified in exosomes, which can be taken up by neighboring or distant cells and subsequently modulate recipient cells. This suggests an active sort-ing mechanism of exosomal miRNAs, since the miRNA profiles of exosomes may differ from those of the parent cells. Exosomal miRNAs play an important role in disease progression, and can stimu-late angiogenesis and facilitate metastasis in cancers. In this review, we will introduce the origin and the trafficking of exosomes between cells, display current research on the sorting mechanism of exo-somal miRNAs, and briefly describe how exosomes and their miRNAs function in recipient cells. Finally, we will discuss the potential applications of these miRNA-containing vesicles in clinical settings.

  16. Psychometric properties of the Arab Heritage Activity Card Sort. (United States)

    Hamed, Razan; Holm, Margo B


    The Activity Card Sort is a valid and reliable assessment tool that was created to assess Participation. It has been translated to several languages and adapted to different international cultures. The most recent version of this tool is the Arabic Heritage Activity Card Sort (A-ACS). The purpose of this study was to establish the psychometric properties of the new Arabic version in Jordanian adults. Forty three Jordanian patients with multiple sclerosis (MS) and 62 healthy adults were recruited to test the psychometric properties of the tool. The A-ACS correlated moderately with the participation index of the Mayo-Portland Adaptability Inventory (r = -0.458, p Heritage of the Activity Card Sort is a valid and reliable tool for Arabic-speaking occupational therapists to use when assessing participation in Jordanian patients with MS or healthy adults. Limitations of this study include using only one diagnostic group from Jordan and examining only the Recovery and Community Versions of the tool. Future studies are needed to examine further psychometric properties for patients with different diagnoses and from different countries in the Arabic region for all three versions of the A-ACS.

  17. Towards high-throughput microfluidic Raman-activated cell sorting. (United States)

    Zhang, Qiang; Zhang, Peiran; Gou, Honglei; Mou, Chunbo; Huang, Wei E; Yang, Menglong; Xu, Jian; Ma, Bo


    Raman-activated cell sorting (RACS) is a promising single-cell analysis technology that is able to identify and isolate individual cells of targeted type, state or environment from an isogenic population or complex consortium of cells, in a label-free and non-invasive manner. However, compared with those widely used yet labeling-required or staining-dependent cell sorting technologies such as FACS and MACS, the weak Raman signal greatly limits the further development of the existing RACS systems to achieve higher throughput. Strategies that can tackle this bottleneck include, first, improvement of Raman-acquisition efficiency and quality based on advanced Raman spectrometers and enhanced Raman techniques; second, development of novel microfluidic devices for cell sorting followed by integration into a complete RACS system. Exploiting these strategies, prototypes for a new generation of RACS have been demonstrated, such as flow-based OT-RACS, DEP-RACS, and SERS/CARS flow cytometry. Such high-throughput microfluidic RACS can provide biologists with a powerful single-cell analysis tool to explore the scientific questions or applications that have been beyond the reach of FACS and MACS.

  18. Sort-Mid tasks scheduling algorithm in grid computing

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda


    Full Text Available Scheduling tasks on heterogeneous resources distributed over a grid computing system is an NP-complete problem. The main aim for several researchers is to develop variant scheduling algorithms for achieving optimality, and they have shown a good performance for tasks scheduling regarding resources selection. However, using of the full power of resources is still a challenge. In this paper, a new heuristic algorithm called Sort-Mid is proposed. It aims to maximizing the utilization and minimizing the makespan. The new strategy of Sort-Mid algorithm is to find appropriate resources. The base step is to get the average value via sorting list of completion time of each task. Then, the maximum average is obtained. Finally, the task has the maximum average is allocated to the machine that has the minimum completion time. The allocated task is deleted and then, these steps are repeated until all tasks are allocated. Experimental tests show that the proposed algorithm outperforms almost other algorithms in terms of resources utilization and makespan.

  19. Thermochemical Pretreatment for Anaerobic Digestion of Sorted Waste (United States)

    Hao, W.; Hongtao, W.


    The effect of alkaline hydrothermal pre-treatment for anaerobic digestion of mechanically-sorted municipal solid waste (MSW) and source-sorted waste was studied. Waste was hydrothermally pre-treated in dilute alkali solution. Hydrolysis product was incubated in 500 ml saline bottle to determine methane potential (MP) under mesospheric anaerobic conditions. Optimum reaction condition obtained in the study is 170 °C at the dose of 4 g NaOH/100 g solid for one hour. Soluble COD was 13936 mg/L and methane yield was 164 ml/g VS for 6 days incubation at optimum conditions. More than 50% biogas increase was achieved over the control, and methane conversion ratio on carbon basis was enhanced to 30.6%. The digestion period was less than 6 days when pre-treatment temperature was above 130 °C. The organic part of sorted waste is mainly constituted of kitchen garbage and leaf. Model kitchen garbage was completely liquidized at 130 °C for one hour and the methane yield was 276 ml/g VS. Addition of alkali enhance hydroxylation rate and methane yield slightly. The biogas potential of leaf could be observed by pre-treatment above 150 °C under alkaline condition.

  20. Differential evolution enhanced with multiobjective sorting-based mutation operators. (United States)

    Wang, Jiahai; Liao, Jianjun; Zhou, Ying; Cai, Yiqiao


    Differential evolution (DE) is a simple and powerful population-based evolutionary algorithm. The salient feature of DE lies in its mutation mechanism. Generally, the parents in the mutation operator of DE are randomly selected from the population. Hence, all vectors are equally likely to be selected as parents without selective pressure at all. Additionally, the diversity information is always ignored. In order to fully exploit the fitness and diversity information of the population, this paper presents a DE framework with multiobjective sorting-based mutation operator. In the proposed mutation operator, individuals in the current population are firstly sorted according to their fitness and diversity contribution by nondominated sorting. Then parents in the mutation operators are proportionally selected according to their rankings based on fitness and diversity, thus, the promising individuals with better fitness and diversity have more opportunity to be selected as parents. Since fitness and diversity information is simultaneously considered for parent selection, a good balance between exploration and exploitation can be achieved. The proposed operator is applied to original DE algorithms, as well as several advanced DE variants. Experimental results on 48 benchmark functions and 12 real-world application problems show that the proposed operator is an effective approach to enhance the performance of most DE algorithms studied.

  1. Digestibility Improvement of Sorted Waste with Alkaline Hydrothermai Pretreatment

    Institute of Scientific and Technical Information of China (English)

    WANG Hao; WANG Hongtao; LU Wenjing; ZHAO Yan


    The digestibility of sorted municipal solid waste (MSW) is often limited by the high content of structured green waste. The objectives of this study are to investigate the effect of alkaline hydrothermal pretreatment on the anaerobic digestion of sorted waste and to analyze the biogas production of different parts of the waste. The waste was hydrothermally pretreated in a dilute alkali solution. The hydrolysis product was then incubated in a 500 mL saline bottle to determine the biochemical methane potential (BMP) under mesophilic anaerobic conditions. The optimum hydrothermal condition was 170℃ at 4 g NaOH/100 g solid for one hour. The concentration of chemical oxygen demand (COD) was 13 936 mg/L and the methane yield was 164 mL/g volatile solid (VS) for 6 days incubation at the optimum conditions. The biogas production was increased more than 50% over the control, with the methane conversion ratio on a carbon basis enhanced to 30.6%. The organic part of the sorted waste was mainly kitchen garbage and leaves. Model kitchen garbage completely liquified at 130℃ for one hour had a methane yield of 276 mL/g VS. The alkali addition slightly enhanced the hydrolyzation rate and methane yield. The biogas potential of leaves was improved by pre-treatment at above 150℃ under alkaline conditions.

  2. Chromosome fragility in Freemartin cattle

    Directory of Open Access Journals (Sweden)

    V. Barbieri


    Full Text Available The aim of the present study was to verify chromosome fragility in freemartin cattle using chromosome aberration (CA and sister chromatid exchange (SCE tests. A total of eighteen co-twins were investigated. Fourteen animals were identified as cytogenetically chimeric (2n=60, XX/XY while 4 were classified as normal. Freemartin cattle showed a higher percentage of aneuploid cells (18.64% and highly significant statistical differences (P < 0.001 in mean values of gaps (4.53 ± 2.05, chromatid breaks (0.26 ± 0.51, and significant statistical differences (P < 0.005 in mean values of chromosome breaks (0.12 ± 0.43 when compared to 10 control animals from single births (aneuploid cells, 11.20%; gaps, 2.01 ± 1.42; chromatid breaks, 0.05 ± 0.22; chromosome breaks, 0.02 ± 0.14.

  3. Enhancing the Executive Functions of 3-Year-Olds in the Dimensional Change Card Sort Task (United States)

    Perone, Sammy; Molitor, Stephen J.; Buss, Aaron T.; Spencer, John P.; Samuelson, Larissa K.


    Executive functions enable flexible thinking, something young children are notoriously bad at. For instance, in the dimensional change card sort (DCCS) task, 3-year-olds can sort cards by one dimension (shape), but continue to sort by this dimension when asked to switch (to color). This study tests a prediction of a dynamic neural field model that…

  4. Lazarus's BASIC ID: Making Initial Client Assessments Using Q-Sorts. (United States)

    Miller, Mark J.


    Presents overview of Lazarus's multimodal therapy model and the Q-sort, an observer-evaluation scoring instrument. Outlines feasibility of integrating Q-sort within multimodal model. Describes both a preliminary attempt using expert raters to categorize Q-sort cards within the model and a case study on how to assess client by incorporating Q-sort…

  5. Chromosome Segregation in Vibrio cholerae


    Ramachandran, R.; Jha, J.; Chattoraj, DK


    The study of chromosome segregation is currently one of the most exciting research frontiers in cell biology. In this review, we discuss our current knowledge of the chromosome segregation process in Vibrio cholerae, based primarily on findings from fluorescence microscopy experiments. This bacterium is of special interest because of its eukaryotic feature of having a divided genome, a feature shared with 10% of known bacteria. We also discuss how the segregation mechanisms of V. cholerae com...

  6. Limiting Index Sort: A New Non-Dominated Sorting Algorithm and its Comparison to the State-of-the-Art (United States)


    dominé (NSGA-II). Nous introduisons l’algorithme Limiting Index Sort (LIS) et démontrons sa supériorité pour le tri des données positivement corrélés démontrons sa supériorité pour le tri des données positivement corrélées ou décorrélées. LIS indexe les solutions individuelles sur la base de...Limiting Index Sort (LIS) et démontrons sa supériorité pour le tri des données positivement corrélés ou décorrélés. LIS indexe les solutions individuelles

  7. B chromosomes and sex in animals. (United States)

    Camacho, J P M; Schmid, M; Cabrero, J


    Supernumerary (B) chromosomes are dispensable elements found in many eukaryote genomes in addition to standard (A) chromosomes. In many respects, B chromosomes resemble sex chromosomes, so that a common ancestry for them has frequently been suggested. For instance, B chromosomes in grasshoppers, and other insects, show a pycnotic cycle of condensation-decondensation during meiosis remarkably similar to that of the X chromosome. In some cases, B chromosome size is even very similar to that of the X chromosome. These resemblances have led to suggest the X as the B ancestor in many cases. In addition, sex chromosome origin from B chromosomes has also been suggested. In this article, we review the existing evidence for both evolutionary pathways, as well as sex differences for B frequency at adult and embryo progeny levels, B chromosome effects or B chromosome transmission. In addition, we review cases found in the literature showing sex-ratio distortion associated with B chromosome presence, the most extreme case being the paternal sex ratio (PSR) chromosomes in some Hymenoptera. We finally analyse the possibility of B chromosome regularisation within the host genome and, as a consequence of it, whether B chromosomes can become regular members of the host genome.

  8. Origin and domestication of papaya Yh chromosome (United States)

    Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XYh). The hermaphrodite-specific region of the Yh chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previo...

  9. Experimental investigation of gravity effects on sediment sorting on Mars (United States)

    Kuhn, Nikolaus J.; Kuhn, Brigitte; Gartmann, Andres


    Introduction: Sorting of sedimentary rocks is a proxy for the environmental conditions at the time of deposition, in particular the runoff that moved and deposited the material forming the rocks. Settling of sediment in water is strongly influenced by the gravity of a planetary body. As a consequence, sorting of a sedimentary rock varies with gravity for a given depth and velocity of surface runoff. Theoretical considerations for spheres indicate that sorting is more uniform on Mars than on Earth for runoff of identical depth. In reality, such considerations have to be applied with great caution because the shape of a particle strongly influences drag. Drag itself can only be calculated directly for an irregularly shaped particle with great computational effort, if at all. Therefore, even for terrestrial applications, sediment settling velocities are often determined directly, e.g. by measurements using settling tubes. Experiments: In this study the results of settling tube tests conducted under reduced gravity during three Mars Sedimentation Experiment (MarsSedEx I, II and III) flights, conducted between 2012 and 2015, are presented. Ten types of sediment, ranging in size, shape and density were tested in custom-designed settling tubes during parabolas of Martian gravity lasting 20 to 25 seconds. Results: The experiments conducted during the MarsSedEx reduced gravity experiments showed that the violation of fluid dynamics caused by using empirical models and parameter values developed for sediment transport on Earth lead to significant miscalculations for Mars, specifically an underetsimation of settling velcoity because of an overestimation of turbulant drag. The error is caused by the flawed representation of particle drag on Mars. Drag coefficients are not a property of a sediment particle, but a property of the flow around the particle, and thus strongly affected by gravity. Conlcusions: The observed errors in settling velocity when using terrestrial models

  10. Bubble-sort图和Modified Bubble-sort图的自同构群%Automorphism Groups of Bubble-sort Graphs and Modified Bubble-sort Graphs

    Institute of Scientific and Technical Information of China (English)

    张昭; 黄琼湘


    Bubble-sort graphs and modified bubble-sort graphs are two classes of Cayley graphs which are widely studied for their application in network construction. In this paper, we determine the full automorphism groups of bubble-sort graphs and modified bubble-sort graphs.%Bubble-Sort图和Modified Bubble-Sort图是两类特殊的Cayley图,由于其在网络构建中的应用而受到广泛关注.本文完全确定了这两类图的自同构群.

  11. Numerically abnormal chromosome constitutions in humans

    Energy Technology Data Exchange (ETDEWEB)



    Chapter 24, discusses numerically abnormal chromosome constitutions in humans. This involves abnormalities of human chromosome number, including polyploidy (when the number of sets of chromosomes increases) and aneuploidy (when the number of individual normal chromosomes changes). Chapter sections discuss the following chromosomal abnormalities: human triploids, imprinting and uniparental disomy, human tetraploids, hydatidiform moles, anomalies caused by chromosomal imbalance, 13 trisomy (D{sub 1} trisomy, Patau syndrome), 21 trisomy (Down syndrome), 18 trisomy syndrome (Edwards syndrome), other autosomal aneuploidy syndromes, and spontaneous abortions. The chapter concludes with remarks on the nonrandom participation of chromosomes in trisomy. 69 refs., 3 figs., 4 tabs.

  12. Low rate of genomic repatterning in Xenarthra inferred from chromosome painting data. (United States)

    Dobigny, G; Yang, F; O'Brien, P C M; Volobouev, V; Kovács, A; Pieczarka, J C; Ferguson-Smith, M A; Robinson, T J


    Comparative cytogenetic studies on Xenarthra, one of the most basal mammalian clades in the Placentalia, are virtually absent, being restricted largely to descriptions of conventional karyotypes and diploid numbers. We present a molecular cytogenetic comparison of chromosomes from the two-toed (Choloepus didactylus, 2n = 65) and three-toed sloth species (Bradypus tridactylus, 2n = 52), an anteater (Tamandua tetradactyla, 2n = 54) which, together with some data on the six-banded armadillo (Euphractus sexcinctus, 2n = 58), collectively represent all the major xenarthran lineages. Our results, based on interspecific chromosome painting using flow-sorted two-toed sloth chromosomes as painting probes, show the sloth species to be karyotypically closely related but markedly different from the anteater. We also test the synteny disruptions and segmental associations identified within Pilosa (anteaters and sloths) against the chromosomes of the six-banded armadillo as outgroup taxon. We could thus polarize the 35 non-ambiguously identified chromosomal changes characterizing the evolution of the anteater and sloth genomes and map these to a published sequence-based phylogeny for the group. These data suggest a low rate of genomic repatterning when placed in the context of divergence estimates based on molecular and fossil data. Finally, our results provide a glimpse of a likely ancestral karyotype for the extant Xenarthra, a pivotal group for understanding eutherian genome evolution.

  13. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. (United States)

    Tomaszkiewicz, Marta; Rangavittal, Samarth; Cechova, Monika; Campos Sanchez, Rebeca; Fescemyer, Howard W; Harris, Robert; Ye, Danling; O'Brien, Patricia C M; Chikhi, Rayan; Ryder, Oliver A; Ferguson-Smith, Malcolm A; Medvedev, Paul; Makova, Kateryna D


    The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.

  14. On the Origin and Evolution of the Extant System of B Chromosomes in Oryzomyini Radiation (Rodentia, Sigmodontinae). (United States)

    Ventura, Karen; O'Brien, Patricia Caroline Mary; do Nascimento Moreira, Camila; Yonenaga-Yassuda, Yatiyo; Ferguson-Smith, Malcolm Andrew


    Heterogeneous supernumerary chromosomes (Bs) are recognized in the oryzomyines Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens and Sooretamys angouya, representing about 10% of all known B-containing rodent species. They provide an outstanding model for understanding the origin, evolution and diversity of Bs in a phylogenetic context. Therefore, whole chromosome-specific probes were generated from flow-sorted Holochilus brasiliensis (HBR) autosomes 11 and 25+26 and chromosomes X, Y and Bs. Hybridizations were performed on male metaphases of 15 Oryzomyini species of which 3 are B-containing species. The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes. The OSHR is also present on Bs of Holochilus brasiliensis, Nectomys rattus and N. squamipes but not on Bs of O. flavescens and S. angouya. Two distinct additional OSHR/autosome associations are observed on S. angouya. The three species that are OSHR negative belong to an outgroup. Molecular dating suggests that the OSHR originated between 7.8 and 3 Mya on ancestral sex chromosomes. A tentative explanation for the OSHR-positive nature of B regions in three species could be that transposable elements (TEs) from this specific sex chromosome region may have invaded existing B chromosomes. The presence of the OSHR on entire Xp and Yp adjacent to interstitial telomeric sequences at pericentromeric positions, as observed in Drymoreomys albimaculatus, show a similar organization as on B chromosomes in Nectomys squamipes. The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys

  15. Safe sorting of GFP-transduced live cells for subsequent culture using a modified FACS vantage

    DEFF Research Database (Denmark)

    Sørensen, T U; Gram, G J; Nielsen, S D;


    culture. RESULTS: The bacteriophage sorting showed that the biologically active material was confined to the sorting chamber. A failure mode simulating a nozzle blockage resulted in detectable droplets inside the sorting chamber, but no droplets could be detected when an additional air suction from....... Safety tests with bacteriophages were performed to evaluate the potential spread of biologically active material during cell sorting. Cells transduced with a retroviral vector carrying the gene for GFP were sorted on the basis of their GFP fluorescence, and GFP expression was followed during subsequent...

  16. Chromosome therapy. Correction of large chromosomal aberrations by inducing ring chromosomes in induced pluripotent stem cells (iPSCs). (United States)

    Kim, Taehyun; Bershteyn, Marina; Wynshaw-Boris, Anthony


    The fusion of the short (p) and long (q) arms of a chromosome is referred to as a "ring chromosome." Ring chromosome disorders occur in approximately 1 in 50,000-100,000 patients. Ring chromosomes can result in birth defects, mental disabilities, and growth retardation if additional genes are deleted during the formation of the ring. Due to the severity of these large-scale aberrations affecting multiple contiguous genes, no possible therapeutic strategies for ring chromosome disorders have so far been proposed. Our recent study (Bershteyn et al.) using patient-derived fibroblast lines containing ring chromosomes, found that cellular reprogramming of these fibroblasts into induced pluripotent stem cells (iPSCs) resulted in the cell-autonomous correction of the ring chromosomal aberration via compensatory uniparental disomy (UPD). These observations have important implications for studying the mechanism of chromosomal number control and may lead to the development of effective therapies for other, more common, chromosomal aberrations.

  17. Inherited unbalanced structural chromosome abnormalities at prenatal chromosome analysis are rarely ascertained through recurrent miscarriage

    NARCIS (Netherlands)

    Franssen, M. T. M.; Korevaar, J. C.; Tjoa, W. M.; Leschot, N. J.; Bossuyt, P. M. M.; Knegt, A. C.; Suykerbuyk, R. F.; Hochstenbach, R.; van der Veen, F.; Goddijn, M.


    Objective To determine the mode of ascertainment of inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis. Methods From the databases of three centres for clinical genetics in the Netherlands, all cases of inherited unbalanced structural chromosome abnorma

  18. An ultrasensitive sorting mechanism for EGF Receptor Endocytosis

    Directory of Open Access Journals (Sweden)

    Dikic Ivan


    Full Text Available Abstract Background The Epidermal Growth Factor (EGF receptor has been shown to internalize via clathrin-independent endocytosis (CIE in a ligand concentration dependent manner. From a modeling point of view, this resembles an ultrasensitive response, which is the ability of signaling networks to suppress a response for low input values and to increase to a pre-defined level for inputs exceeding a certain threshold. Several mechanisms to generate this behaviour have been described theoretically, the underlying assumptions of which, however, have not been experimentally demonstrated for the EGF receptor internalization network. Results Here, we present a mathematical model of receptor sorting into alternative pathways that explains the EGF-concentration dependent response of CIE. The described mechanism involves a saturation effect of the dominant clathrin-dependent endocytosis pathway and implies distinct steady-states into which the system is forced for low vs high EGF stimulations. The model is minimal since no experimentally unjustified reactions or parameter assumptions are imposed. We demonstrate the robustness of the sorting effect for large parameter variations and give an analytic derivation for alternative steady-states that are reached. Further, we describe extensibility of the model to more than two pathways which might play a role in contexts other than receptor internalization. Conclusion Our main result is that a scenario where different endocytosis routes consume the same form of receptor corroborates the observation of a clear-cut, stimulus dependent sorting. This is especially important since a receptor modification discriminating between the pathways has not been found experimentally. The model is not restricted to EGF receptor internalization and might account for ultrasensitivity in other cellular contexts.

  19. Numerical Model of Streaming DEP for Stem Cell Sorting

    Directory of Open Access Journals (Sweden)

    Rucha Natu


    Full Text Available Neural stem cells are of special interest due to their potential in neurogenesis to treat spinal cord injuries and other nervous disorders. Flow cytometry, a common technique used for cell sorting, is limited due to the lack of antigens and labels that are specific enough to stem cells of interest. Dielectrophoresis (DEP is a label-free separation technique that has been recently demonstrated for the enrichment of neural stem/progenitor cells. Here we use numerical simulation to investigate the use of streaming DEP for the continuous sorting of neural stem/progenitor cells. Streaming DEP refers to the focusing of cells into streams by equilibrating the dielectrophoresis and drag forces acting on them. The width of the stream should be maximized to increase throughput while the separation between streams must be widened to increase efficiency during retrieval. The aim is to understand how device geometry and experimental variables affect the throughput and efficiency of continuous sorting of SC27 stem cells, a neurogenic progenitor, from SC23 cells, an astrogenic progenitor. We define efficiency as the ratio between the number of SC27 cells over total number of cells retrieved in the streams, and throughput as the number of SC27 cells retrieved in the streams compared to their total number introduced to the device. The use of cylindrical electrodes as tall as the channel yields streams featuring >98% of SC27 cells and width up to 80 µm when using a flow rate of 10 µL/min and sample cell concentration up to 105 cells/mL.

  20. Depth optimal sorting networks resistant to k passive faults

    Energy Technology Data Exchange (ETDEWEB)

    Piotrow, M. [Univ. of Wroclaw (Poland)


    In this paper, we study the problem of constructing a sorting network that is tolerant to faults and whose running time (i.e. depth) is as small as possible. We consider the scenario of worst-case comparator faults and follow the model of passive comparator failure proposed by Yao and Yao, in which a faulty comparator outputs directly its inputs without comparison. Our main result is the first construction of an N-input, k-fault-tolerant sorting network that is of an asymptotically optimal depth {theta}(log N+k). That improves over the recent result of Leighton and Ma, whose network is of depth O(log N + k log log N/log k). Actually, we present a fault-tolerant correction network that can be added after any N-input sorting network to correct its output in the presence of at most k faulty comparators. Since the depth of the network is O(log N + k) and the constants hidden behind the {open_quotes}O{close_quotes} notation are not big, the construction can be of practical use. Developing the techniques necessary to show the main result, we construct a fault-tolerant network for the insertion problem. As a by-product, we get an N-input, O(log N)-depth INSERT-network that is tolerant to random faults, thereby answering a question posed by Ma in his PhD thesis. The results are based on a new notion of constant delay comparator networks, that is, networks in which each register is used (compared) only in a period of time of a constant length. Copies of such networks can be put one after another with only a constant increase in depth per copy.

  1. Preliminary Results on Sediment Sorting Under Intense Bedload Transport (United States)

    Hernandez Moreira, R. R.; Vautin, D.; Mathews, S. L.; Kuprenas, R.; Viparelli, E.


    Previous experiments show that parallel-laminated deposits are emplaced under upper plane bed regime by the migration of small-amplitude, long-wavelength bedforms. The present research focuses on how sediment is sorted under upper plane bed and sheet flow transport regimes, and whether parallel-lamination is inhibited during sheet flow transport. The problem of studying the sorting of sediment under so intense transport conditions is plagued by the uncertainties related to flow resistances and bedload transport rates. We simplify the problem by first running the experiments with uniform sediment, to establish a baseline that will aid in the design of the experiments with poorly sorted material. We are running experiments at the Hydraulics Laboratory of the Department of Civil and Environmental Engineering at the University of South Carolina in Columbia, in a unidirectional sediment-feed flume, 9 meters long by 0.2 meters wide, of which 7 meters are used as test section. During the experiments, water surface and bed elevations are periodically measured to characterize the global parameters of the flow, e.g. mean flow velocity and bed shear stress. When the flow and the sediment transport reach conditions of mobile bed equilibrium, bed elevation fluctuations are measured with ultrasonic transducer systems at six fixed locations. Channel bed aggradation is then induced by slowly raising the tail gate of the flume such that there is no change in transport regime, as confirmed by additional measurements of water surface and bed elevation and bed elevation fluctuations. Preliminary observations under upper plane bed regime show the formation of the small-amplitude and long-wavelength bedforms, as well as hints of parallel lamination in the deposits. In the near future we aim to achieve sheet flow transport conditions with both uniform and non-uniform grain size distributions to look at the internal structure of the emplaced deposit.

  2. Study for standardization of the lighting system in fruit sorting (United States)

    Gomes, J. F. S.; Baldner, F. O.; Costa, P. B.; Guedes, M. B.; Oliveira, I. A. A.; Leta, F. R.


    Sorting is a very important step in the fruit processing. The attributes definition and characterization are important for both marketing and end user, making it necessary to establish regulations for classification and standardization in order to unify the language of the market and enabling a more efficient market and also increase consumer awareness. For this end, it is necessary to standardize the technical criteria that can change the perception of the product. Studies have been developed in order to standardize a methodology to determine the subclass of fruit ripening, evaluating the influence of different light sources in the subclass evaluation.

  3. Cholesterol-induced protein sorting: an analysis of energetic feasibility

    DEFF Research Database (Denmark)

    Lundbaek, J A; Andersen, O S; Werge, T


    The mechanism(s) underlying the sorting of integral membrane proteins between the Golgi complex and the plasma membrane remain uncertain because no specific Golgi retention signal has been found. Moreover one can alter a protein's eventual localization simply by altering the length of its...... thickness. In this model, Golgi proteins with short TMDs would be excluded from cholesterol-enriched domains (lipid rafts) that are incorporated into transport vesicles destined for the plasma membrane. Although attractive, this model remains unproven. We therefore evaluated the energetic feasibility...

  4. Airborne microorganisms associated with packaging glass sorting facilities. (United States)

    Pinto, Marta Jorge de Vasconcelos; Veiga, José Miguel; Fernandes, Paulo; Ramos, Carla; Gonçalves, Sérgio; Velho, Maria Manuela Lemos Vaz; Guerreiro, Joana Santos


    In recent years, efforts have been undertaken to reduce the volume of residual waste through sorting and recycling. The waste management and recycling sector is thriving and the number of workers there is increasing. In this context, prior knowledge of the risks to which workers may be exposed is of crucial importance, and preventive measures need to be put in place to accurately identify and quantify those risks. This study aimed to assess occupational risk of exposure to biological agents (viable bacteria and fungi) in a Portuguese waste packaging glass sorting plant. Air samples were collected from selected locations in waste sorting cabins (critical area, CA), administrative services (noncritical area, NCA) and outdoors (control point, CP). Duplicate air samples were collected through an impaction method. The investigation was carried out over an 8-mo period with two collection periods, autumn/winter (AW) and spring/summer (SS), in order to access the influence of any seasonal variation. In the 36 air samples collected, 319 bacterial and 196 mold identifications were performed. Air samples revealed existence of high environmental contamination by bacteria (1.6 × 10(4) colony forming units [cfu]/m(3)) and fungi (1.5 × 10(4) cfu/m(3)). The predominant bacterial genus was Staphylococcus (coagulase negative) with values ranging from 29.6 to 60% of the total count of bacteria. Genera Bacillus, Micrococcus, and Staphylococcus (coagulase negative) were also present at all sampling sites, regardless of the season. However, the counts of these genera, in the CA, were higher in warmer seasons. The genus Penicillium was the most frequent genus present with an approximate value of 95% of total fungal count in the CA. Seasonal variation was a significant factor for total bacteria and fungi, except for NCA versus CP. Overall, the highest levels of bacterial and fungal species (10(4) cfu/m(3)) were found in the waste sorting cabin (CA). These results highlight the

  5. BSSSN: Bit String Swapping Sorting Network for Reversible Logic Synthesis

    CERN Document Server

    Islam, Md Saiful


    In this paper, we have introduced the notion of UselessGate and ReverseOperation. We have also given an algorithm to implement a sorting network for reversible logic synthesis based on swapping bit strings. The network is constructed in terms of n*n Toffoli Gates read from left to right and it has shown that there will be no more gates than the number of swappings the algorithm requires. The gate complexity of the network is O(n2). The number of gates in the network can be further reduced by template reduction technique and removing UselessGate from the network.

  6. Insight into economies of scale for waste packaging sorting plants

    DEFF Research Database (Denmark)

    Cimpan, Ciprian; Wenzel, Henrik; Maul, Anja


    This contribution presents the results of a techno-economic analysis performed for German Materials Recovery Facilities (MRFs) which sort commingled lightweight packaging waste (consisting of plastics, metals, beverage cartons and other composite packaging). The study addressed the importance...... of economies of scale and discussed complementary relations occurring between capacity size, technology level and operational practice. Processing costs (capital and operational expenditure) per unit waste input were found to decrease from above 100 € for small plants with a basic technology level to 60...

  7. Size Sorting on the Rubble-Pile Asteroid Itokawa (United States)

    Shinbrot, Troy; Sabuwala, Tapan; Siu, Theo; Vivar Lazo, Miguel; Chakraborty, Pinaki


    Photographs of the asteroid Itokawa reveal unexpectedly strong size segregation between lowlands populated almost entirely by small pebbles and highlands consisting of larger boulders. We propose that this segregation may be caused by a simple and unexplored effect: pebbles accreting onto the asteroid rebound from boulders, but sink into pebbly regions. By number, overwhelmingly more particles on Itokawa are pebbles, and collisions involving these pebbles must unavoidably cause pebbly regions to grow. We carry out experiments and simulations that demonstrate that this mechanism of size sorting based on simple counting of grains produces strong lateral segregation that reliably obeys an analytic formula.

  8. Shrink-induced sorting using integrated nanoscale magnetic traps. (United States)

    Nawarathna, Dharmakeerthi; Norouzi, Nazila; McLane, Jolie; Sharma, Himanshu; Sharac, Nicholas; Grant, Ted; Chen, Aaron; Strayer, Scott; Ragan, Regina; Khine, Michelle


    We present a plastic microfluidic device with integrated nanoscale magnetic traps (NSMTs) that separates magnetic from non-magnetic beads with high purity and throughput, and unprecedented enrichments. Numerical simulations indicate significantly higher localized magnetic field gradients than previously reported. We demonstrated >20 000-fold enrichment for 0.001% magnetic bead mixtures. Since we achieve high purity at all flow-rates tested, this is a robust, rapid, portable, and simple solution to sort target species from small volumes amenable for point-of-care applications. We used the NSMT in a 96 well format to extract DNA from small sample volumes for quantitative polymerase chain reaction (qPCR).

  9. A Special Sort of Forgetting: Negation in Freud and Augustine. (United States)

    Rosengart, Daniel


    The development from a positive, dualistic theory of memory and forgetting to a concept of memory that includes forgetting as a variety of remembering is traced in two thinkers. Freud's concept of repression is discussed as a complex negation of both remembering and forgetting, and the development of this construct is shown in his letters to Wilhelm Fliess. A close reading of Augustine of Hippo's Confessions shows a similar concept of a special sort of forgetting, in which what is forgotten is remembered nonetheless. Finally, the limits of the comparison are discussed, and a reading of Freud's "Negation" reveals ways in which the unconscious is fundamentally unlike Augustine's interiority.

  10. Dean flow fractionation of chromosomes (United States)

    Hockin, Matt; Sant, Himanshu J.; Capecchi, Mario; Gale, Bruce K.


    Efforts to transfer intact mammalian chromosomes between cells have been attempted for more than 50 years with the consistent result being transfer of sub unit length pieces regardless of method. Inertial microfluidics is a new field that has shown much promise in addressing the fractionation of particles in the 2-20 μm size range (with unknown limits) and separations are based upon particles being carried by curving confined flows (within a spiral shaped, often rectangular flow chamber) and migrating to stable "equilibrium" positions of varying distance from a chamber wall depending on the balance of dean and lift forces. We fabricated spiral channels for inertial microfluidic separations using a standard soft lithography process. The concentration of chromosomes, small contaminant DNA and large cell debris in each outlets were evaluated using microscope (60X) and a flow cytometer. Using Dean Flow Fractionation, we were able to focus 4.5 times more chromosomes in outlet 2 compared to outlet 4 where most of the large debris is found. We recover 16% of the chromosomes in outlet #1- 50% in 2, 23% in 3 and 11% in 4. It should be noted that these estimates of recovery do not capture one piece of information- it actually may be that the chromosomes at each outlet are physically different and work needs to be done to verify this potential.

  11. Chromosome segregation in plant meiosis

    Directory of Open Access Journals (Sweden)

    Linda eZamariola


    Full Text Available Faithful chromosome segregation in meiosis is essential for ploidy stability over sexual life cycles. In plants, defective chromosome segregation caused by gene mutations or other factors leads to the formation of unbalanced or unreduced gametes creating aneuploid or polyploid progeny, respectively. Accurate segregation requires the coordinated execution of conserved processes occurring throughout the two meiotic cell divisions. Synapsis and recombination ensure the establishment of chiasmata that hold homologous chromosomes together allowing their correct segregation in the first meiotic division, which is also tightly regulated by cell-cycle dependent release of cohesin and monopolar attachment of sister kinetochores to microtubules. In meiosis II, bi-orientation of sister kinetochores and proper spindle orientation correctly segregate chromosomes in four haploid cells. Checkpoint mechanisms acting at kinetochores control the accuracy of kinetochore-microtubule attachment, thus ensuring the completion of segregation. Here we review the current knowledge on the processes taking place during chromosome segregation in plant meiosis, focusing on the characterization of the molecular factors involved.

  12. The Reduction of Chromosome Number in Meiosis Is Determined by Properties Built into the Chromosomes


    Paliulis, Leocadia V.; Nicklas, R. Bruce


    In meiosis I, two chromatids move to each spindle pole. Then, in meiosis II, the two are distributed, one to each future gamete. This requires that meiosis I chromosomes attach to the spindle differently than meiosis II chromosomes and that they regulate chromosome cohesion differently. We investigated whether the information that dictates the division type of the chromosome comes from the whole cell, the spindle, or the chromosome itself. Also, we determined when chromosomes can switch from ...

  13. The Sorting Buffer Problem is NP-hard

    CERN Document Server

    Chan, Ho-Leung; van Stee, Rob; Sitters, Rene


    We consider the offline sorting buffer problem. The input is a sequence of items of different types. All items must be processed one by one by a server. The server is equipped with a random-access buffer of limited capacity which can be used to rearrange items. The problem is to design a scheduling strategy that decides upon the order in which items from the buffer are sent to the server. Each type change incurs unit cost, and thus, the cost minimizing objective is to minimize the total number of type changes for serving the entire sequence. This problem is motivated by various applications in manufacturing processes and computer science, and it has attracted significant attention in the last few years. The main focus has been on online competitive algorithms. Surprisingly little is known on the basic offline problem. In this paper, we show that the sorting buffer problem with uniform cost is NP-hard and, thus, close one of the most fundamental questions for the offline problem. On the positive side, we give ...

  14. Exosome and exosomal microRNA: trafficking, sorting, and function. (United States)

    Zhang, Jian; Li, Sha; Li, Lu; Li, Meng; Guo, Chongye; Yao, Jun; Mi, Shuangli


    Exosomes are 40-100 nm nano-sized vesicles that are released from many cell types into the extracellular space. Such vesicles are widely distributed in various body fluids. Recently, mRNAs and microRNAs (miRNAs) have been identified in exosomes, which can be taken up by neighboring or distant cells and subsequently modulate recipient cells. This suggests an active sorting mechanism of exosomal miRNAs, since the miRNA profiles of exosomes may differ from those of the parent cells. Exosomal miRNAs play an important role in disease progression, and can stimulate angiogenesis and facilitate metastasis in cancers. In this review, we will introduce the origin and the trafficking of exosomes between cells, display current research on the sorting mechanism of exosomal miRNAs, and briefly describe how exosomes and their miRNAs function in recipient cells. Finally, we will discuss the potential applications of these miRNA-containing vesicles in clinical settings.

  15. Exosome and Exosomal MicroRNA: Trafficking, Sorting, and Function

    Directory of Open Access Journals (Sweden)

    Jian Zhang


    Full Text Available Exosomes are 40–100 nm nano-sized vesicles that are released from many cell types into the extracellular space. Such vesicles are widely distributed in various body fluids. Recently, mRNAs and microRNAs (miRNAs have been identified in exosomes, which can be taken up by neighboring or distant cells and subsequently modulate recipient cells. This suggests an active sorting mechanism of exosomal miRNAs, since the miRNA profiles of exosomes may differ from those of the parent cells. Exosomal miRNAs play an important role in disease progression, and can stimulate angiogenesis and facilitate metastasis in cancers. In this review, we will introduce the origin and the trafficking of exosomes between cells, display current research on the sorting mechanism of exosomal miRNAs, and briefly describe how exosomes and their miRNAs function in recipient cells. Finally, we will discuss the potential applications of these miRNA-containing vesicles in clinical settings.

  16. Design and construction of automatic sorting station with machine vision

    Directory of Open Access Journals (Sweden)

    Oscar D. Velasco-Delgado


    Full Text Available This article presents the design, construction and testing of an automatic product sorting system in belt conveyor with machine vision that integrates Free and Open Source Software technology and Allen Bradley commercial equipment. Requirements are defined to determine features such as: mechanics of manufacturing station, an app of product sorting with machine vision and for automation system. For the app of machine vision a library is used for optical digital image processing Open CV, for the mechanical design of the manufacturing station is used the CAD tool Solid Edge and for the design and implementation of automation ISA standards are used along with an automation engineering project methodology integrating a PLC, an inverter, a Panel View and a DeviceNet Network. Performance tests are shown by classifying bottles and PVC pieces in four established types, the behavior of the integrated system is checked so as the efficiency of the same. The processing time on machine vision is 0.290 s on average for a piece of PVC, a capacity of 206 accessories per minute, for bottles was obtained a processing time of 0.267 s, a capacity of 224 bottles per minute. A maximum mechanical performance is obtained with 32 products per minute (1920 products/hour with the conveyor to 22 cm/s and 40 cm of distance between products obtaining an average error of 0.8%.

  17. The RCP-Rab11 complex regulates endocytic protein sorting. (United States)

    Peden, Andrew A; Schonteich, Eric; Chun, John; Junutula, Jagath R; Scheller, Richard H; Prekeris, Rytis


    Rab 11 GTPase is an important regulator of endocytic membrane traffic. Recently, we and others have identified a novel family of Rab11 binding proteins, known as Rab11-family interacting proteins (FIPs). One of the family members, Rab coupling protein (RCP), was identified as a protein binding to both Rab4 and Rab11 GTPases. RCP was therefore suggested to serve a dual function as Rab4 and Rab11 binding protein. In this study, we characterized the cellular functions of RCP and mapped its interactions with Rab4 and Rab11. Our data show that RCP interacts only weakly with Rab4 in vitro and does not play the role of coupling Rab11 and Rab4 in vivo. Furthermore, our data indicate that the RCP-Rab11 complex regulates the sorting of transferrin receptors from the degradative to the recycling pathway. We therefore propose that RCP functions primarily as a Rab11 binding protein that regulates protein sorting in tubular endosomes.

  18. A Microfluidic Chip for Liquid Metal Droplet Generation and Sorting

    Directory of Open Access Journals (Sweden)

    Lu Tian


    Full Text Available A liquid metal based microfluidic system was proposed and demonstrated for the generation and sorting of liquid metal droplets. This micro system utilized silicon oil as the continuous phase and Ga66In20.5Sn13.5 (66.0 wt % Ga, 20.5 wt % In, 13.5 wt % Sn, melting point: 10.6 °C as the dispersed phase to generate liquid metal droplets on a three-channel F-junction generator. The F-junction is an updated design similar to the classical T-junction, which has a special branch channel added to a T-junction for the supplement of 30 wt % aqueous NaOH solution. To perform active sorting of liquid metal droplets by dielectrophoresis (DEP, the micro system utilized liquid-metal-filled microchannels as noncontact electrodes to induce electrical fields through the droplet channel. The electrode channels were symmetrically located on both sides of the droplet channel in the same horizontal level. According to the results, the micro system can generate uniformly spherical liquid metal droplets, and control the flow direction of the liquid metal droplets. To better understand the control mechanism, a numerical simulation of the electrical field was performed in detail in this work.

  19. Devices for the production and sorting of microfluidic droplets (United States)

    Aubrecht, Donald; Heyman, John; Agresti, Jeremy; Köster, Sarah; Weitz, David


    Droplets produced in microfluidic devices are a great set of tools for studying large cell populations and permutations of reactions. Sample populations of 10^6 - 10^7 can be studied with relative ease, as encapsulation and screening rates in the kHz range are accessible. Previous droplet work has shown encapsulation of cells in droplets allows individual cells and their products to be studied. Advantages include correlation between detected products and initial drop contents, as well as minimized sample cross-contamination. Most microfluidic-based biological assays rely on fluorescent labeling of cells or use of cellular products to initiate a fluorescence-producing reaction. Detection of the fluorescence provides a trigger for sorting those cells or cell-containing droplets away from the general population. Though this allows some cellular processes to be studied, detection and quantification of all products, not just those expressed to the cell surface or those that catalyze reactions, would impact development of better therapeutics. We are currently working to adapt benchtop biological assays that label and detect cellular products for use in a droplet-based system. The work presented here details the chain of modular microfluidic devices we use to encapsulate, incubate, interrogate, and sort a population of droplets containing a model system.

  20. Boar sperm changes after sorting and encapsulation in barium alginate membranes. (United States)

    Spinaci, M; Bucci, D; Chlapanidas, T; Vallorani, C; Perteghella, S; Communod, R; Vigo, D; Tamanini, C; Galeati, G; Faustini, M; Torre, M L


    A routine use of boar-sexed semen is limited by the long sorting time necessary to obtain an adequate number of sexed spermatozoa for artificial insemination and by the high susceptibility of spermatozoa of this species to damages induced by sorting procedure and subsequent cryopreservation. The aim of this work was to study the impact of encapsulation in barium alginate membrane on sorted boar spermatozoa by evaluating membrane integrity, chlortetracycline staining patterns, protein tyrosine phosphorylation, and Hsp70 immunolocalization during storage over 72 hours in liquid or encapsulated form. The encapsulation procedure significantly (P < 0.05) decreased the overall membrane integrity of control unsorted semen (81.8 vs. 57.4, CTR vs. CPS), but did not negatively affect the overall viability and the chlortetracycline staining patterns of sorted encapsulated cells. Moreover, encapsulation significantly decreased (P < 0.05) the overall phosphotyrosin A pattern cell percentage in unsorted (98.4 vs. 92.6, CTR vs. CPS) but not in sorted semen (64.0 vs. 74.2; SORT CTR vs. SORT CPS). As for Hsp70, the overall percentage of cells displaying the different patterns was significantly influenced (P < 0.05) by treatment but not by storage time. The sorting procedure seems to induce the major changes, whereas encapsulation tends to exert a protective effect on sorted semen by increasing the percentage of spermatozoa displaying the T pattern (2.8 vs. 24.3; SORT CTR vs. SORT CPS). In conclusion, our data confirm that the damaging impact of the encapsulation in barium alginate capsules seems to be limited when compared with that of the sorting procedure and, moreover, the association of the two procedures does not result in an algebraic sum of the negative effects. These results suggest the possibility of a future utilization of the encapsulation technology in order to store sorted spermatozoa and permit their controlled release in the female genital tract.

  1. Chromosome-specific families in Vibrio genomes

    Directory of Open Access Journals (Sweden)

    Oksana eLukjancenko


    Full Text Available We have compared chromosome-specific genes in a set of 18 finished Vibrio genomes, and, in addition, also calculated the pan- and core-genomes from a data set of more than 250 draft Vibrio genome sequences. These genomes come from 9 known species and 2 unknown species. Within the finished chromosomes, we find a core set of 1269 encoded protein families for chromosome 1, and a core of 252 encoded protein families for chromosome 2. Many of these core proteins are also found in the draft genomes (although which chromosome they are located on is unknown. Of the chromosome specific core protein families, 1169 and 153 are uniquely found in chromosomes 1 and 2, respectively. Gene ontology (GO terms for each of the protein families were determined, and the different sets for each chromosome were compared. A total of 363 different `Molecular Function` GO categories were found for chromosome 1 specific protein families, and these include several broad activities: pyridoxine 5' phosphate synthetase, glucosylceramidase, heme transport, DNA ligase, amino acid binding, and ribosomal components; in contrast, chromosome 2 specific protein families have only 66 Molecular Function GO terms and include many membrane-associated activities, such as ion channels, transmembrane transporters, and electron transport chain proteins. Thus, it appears that whilst there are many 'housekeeping systems' encoded in chromosome 1, there are far fewer core functions found in chromosome 2. However, the presence of many membrane-associated encoded proteins in chromosome 2 is surprising.

  2. The Cleveland Sorting Test: a preliminary study of an alternate form of the Wisconsin Card-Sorting Test. (United States)

    Poreh, Amir; Pastel, Dan; Miller, Ashley; Levin, Jennifer


    During the past two decades, studies have repeatedly shown that the Wisconsin Card-Sorting Test (WCST) is not as sensitive to prefrontal-lobe functioning as was originally suspected. Specifically, both clinical and brain-imaging studies have shown that several distinct neural circuits contribute to one's ability to successfully complete different aspects of the test. Another limitation of the WCST is its length, which makes it difficult and frustrating for certain clinical populations. To address the above limitations, researchers have proposed the development of new indexes and the integration of an adaptive testing approach that will allow for the premature termination of the test. Unfortunately, given the proprietary nature of the WCST, none of the above recommendations have been adopted. The present preliminary study examined an alternate form of the 64-Item WCST (WCST-64), the Cleveland Sorting Test (CST-64). The normative data of the two measures as well as the total number of errors, perseverative responses, perseverative errors, and categories completed were compared using a repeated-measures design. Overall, the study supports psychometric approximation of the CST-64 and the WCST-64. Suggestions for future studies and modifications of the CST-64, including the use of recently proposed indexes and adaptive administration approaches, are provided.

  3. Sex chromosome rearrangements in Polyphaga beetles. (United States)

    Dutrillaux, A M; Dutrillaux, B


    The presence of a parachute sex chromosome bivalent (Xyp) at metaphase I of male meiosis is a well-known characteristic of Coleoptera, present in almost all families of this order and assumed to represent their ancestral sex chromosome formula. Sex chromosomes appear to be manifold more frequently involved in inter-chromosomal rearrangements than the average of the nine autosomal pairs usually forming their karyotype. This leads to various formulae such as neo-sex, multiple sex and perhaps unique sex chromosomes. These rearrangements alter the intimate association between sex chromosomes and nucleolar proteins, which are usual components of the Xyp. Different situations, selected in a series of 125 mitotic and meiotic cytogenetic studies of Polyphaga beetle species, are reported and discussed, with the aim to improve our knowledge on the mechanisms of sex chromosome rearrangements, the relationships with nucleoli and the consequences on dosage compensation and chromosome segregation.

  4. Vibrio chromosome-specific families

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David


    We have compared chromosome-specific genes in a set of 18 finished Vibrio genomes, and, in addition, also calculated the pan- and core-genomes from a data set of more than 250 draft Vibrio genome sequences. These genomes come from 9 known species and 2 unknown species. Within the finished...

  5. Chromosome Territory Modeller and Viewer. (United States)

    Tkacz, Magdalena A; Chromiński, Kornel; Idziak-Helmcke, Dominika; Robaszkiewicz, Ewa; Hasterok, Robert


    This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.


    We have used CHEF gel electrophoresis to screen preparations of large DNA from different Burkholderia cepacia isolates for the presence of DNA species corresponding to the linearized forms of the three chromosomes of 3.4,2.5, and 0.9 Mb identified in B. cepacia strain 17616. DNA ...

  7. Chromosome synteny in cucumis species (United States)

    Cucumber, Cucumis sativus L. (2n = 2x = 14) and melon, C. melo L. (2n = 2x = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Two inter-fertile botanical varieties with 14 chromosomes, the cultivated C. sativus var. sativus L. and the wild C. sativus var. hardwick...

  8. Chromosomal disorders and male infertility

    Institute of Scientific and Technical Information of China (English)

    Gary L Harton; Helen G Tempest


    infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family.Despite this,the molecular and genetic factors underlying the cause of infertility remain largely undiscovered.Nevertheless,more and more genetic factors associated with infertility are being identified.This review will focus on our current understanding of the chromosomal basis of male infertility specifically:chromosomal aneuploidy,structural and numerical karyotype abnormalities and Y chromosomal microdeletions.Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans.Aneuploidy is predominantly maternal in origin,but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts.Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm.Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed,as well as the application of preimplantation genetic diagnosis (PGD) in such cases.Clinical recommendations where possible will be made,as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.

  9. Finite-size corrections to scaling behavior in sorted cell aggregates. (United States)

    Klopper, A V; Krens, G; Grill, S W; Heisenberg, C-P


    Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect.

  10. Online tomato sorting based on shape, maturity, size, and surface defects using machine vision


    ARJENAKI, Omid Omidi; MOGHADDAM, Parviz Ahmadi; MOTLAGH, Asad Moddares


    Online sorting of tomatoes according to their features is an important postharvest procedure. The purpose of this research was to develop an efficient machine vision-based experimental sorting system for tomatoes. Relevant sorting parameters included shape (oblong and circular), size (small and large), maturity (color), and defects. The variables defining shape, maturity, and size of the tomatoes were eccentricity, average of color components, and 2-D pixel area, respectively. Tomato defects ...

  11. Performance of Children with Autism Spectrum Disorders on the Dimension-Change Card Sort Task


    Dichter, Gabriel S.; Radonovich, Krestin J.; Turner-Brown, Lauren M.; LAM, KRISTEN S. L.; HOLTZCLAW, TIA N.; Bodfish, James W.


    Restricted and repetitive behaviors in autism spectrum disorders have been conceptualized to reflect impaired executive functions. In the present study, we investigated the performance of 6–17-year-old children with and without an autism spectrum disorder on a dimension-change card sort task that explicitly indicated sorting rules on every trial. Diagnostic groups did not differ in speed of responses after the first rule switch or in speed or accuracy on blocks with mixed versus single sort r...

  12. A Plain English Map of the Human Chromosomes. (United States)

    Offner, Susan


    Presents a chromosome map for 19 known chromosomes in human genetics. Describes the characteristics attributed to the genetic codes for each of the chromosomes and discusses the teaching applications of the chromosome map. (MDH)

  13. Familial transmission of a ring chromosome 21

    DEFF Research Database (Denmark)

    Hertz, Jens Michael


    A ring chromosome 21 was found in a phenotypically normal mother and her son. The clinical findings in the son were bilateral retention of the testes and a slightly delayed puberty onset. Consequences of a ring formation of a chromosome 21 in phenotypically normal patients are presented...... and discussed, and the previously reported cases of familially transmitted G-group ring chromosomes are reviewed....

  14. Female meiotic sex chromosome inactivation in chicken

    NARCIS (Netherlands)

    S. Schoenmakers (Sam); E. Wassenaar (Evelyne); J.W. Hoogerbrugge (Jos); J.S.E. Laven (Joop); J.A. Grootegoed (Anton); W.M. Baarends (Willy)


    textabstractDuring meiotic prophase in male mammals, the heterologous X and Y chromosomes remain largely unsynapsed, and meiotic sex chromosome inactivation (MSCI) leads to formation of the transcriptionally silenced XY body. In birds, the heterogametic sex is female, carrying Z and W chromosomes (Z

  15. Optimum Identification Method of Sorting Green Household Waste

    Directory of Open Access Journals (Sweden)

    Daud Mohd Hisam


    Full Text Available This project is related to design of sorting facility for reducing, reusing, recycling green waste material, and in particular to invent an automatic system to distinguish household waste in order to separate them from the main waste stream. The project focuses on thorough analysis of the properties of green household waste. The method of identification is using capacitive sensor where the characteristic data taken on three different sensor drive frequency. Three types of material have been chosen as a medium of this research, to be separated using the selected method. Based on capacitance characteristics and its ability to penetrate green object, optimum identification method is expected to be recognized in this project. The output capacitance sensor is in analogue value. The results demonstrate that the information from the sensor is enough to recognize the materials that have been selected.

  16. Increased Sorting and Wage Inequality in the Czech Republic

    DEFF Research Database (Denmark)

    Eriksson, Tor; Pytlikova, Mariola; Warzynski, Frederic Michel Patrick


    This paper makes use of a linked employer–employee dataset to examine the evolution of wage inequality in the Czech Republic during 1998–2006. We find evidence of slightly increasing returns to human capital and diminishing gender inequality and document sharp increases in both within......-firm and between-firm inequality. We investigate several hypotheses to explain these patterns: increased domestic and international competition, decentralized wage bargaining, skill-biased technological change and a changing educational composition of the workforce. Domestic competition is found to lower within......-firm inequality whereas we find no evidence that increased international trade at the industry level is associated with higher betweenor within-firm wage inequality. The key factors driving the observed increase in wage inequality are increased educational sorting and the inflow of foreign firms to the Czech...

  17. Magnetic activated cell sorting (MACS): utility in assisted reproduction. (United States)

    Makker, Kartikeya; Agarwal, Ashok; Sharma, Rakesh K


    Assisted reproductive techniques (ART) have now been extensively incorporated in the management of infertile couples. But even after rapid methodological and technological advances the success rates of these procedures have been below expectations. This has led to development of many sperm preparation protocols to obtain an ideal semen sample for artificial reproduction. Sperm apoptosis has been heavily linked to failures in reproductive techniques. One of the earliest changes shown by apoptotic spermatozoa is externalization of phosphatidyl serine. Magnetic activated cell sorting (MACS) is a novel sperm preparation technique that separates apoptotic and non-apoptotic spermatozoa based on the expression of phosphatidylserine. This has led to the incorporation of MACS as a sperm preparation technique. The review highlights the principle and mechanism of this novel technique and enumerates its advantages as a sperm preparation technique. Its utility in ART as an efficient tool for sperm recovery and its application in cryopreservation of semen samples is also explained.

  18. Improved Sorting Scheme of Microstructure of Fly Ash

    Institute of Scientific and Technical Information of China (English)

    王立刚; 彭苏平


    Aiming at the problem of the existing sorting for microstructure of flyash, an improved scheme was put forward in this paper. First, fly ash particles are divided into four groups as low-calcium, iron, high calcium and char particle acco rding to the substance components of fly ash. Then fly ash particles are divided into 14 sub-groups, for example: cenospheres, plerospheres, solid spheres, porous char and dense char based on their chemical composition, shape and the chara cteristics of inner-structure of fly ash. It has a distinct difference in granu le configuration, inner-structure and substance components. Some disadvantages of the existing scheme such as unilateralism and imprecision have been overcome in the advanced schemes.

  19. Collaborative Product Design for Tasks Sorting Based on Shortest Delivery

    Directory of Open Access Journals (Sweden)

    Xuedong Liang


    Full Text Available The “people’s innovation” can promote development in enterprises in urgent need of innovative product design. Collaborative product design can be a powerful tool for enterprises wishing to improve their market competitiveness and customer satisfaction. To reduce decision costs, improve efficiency, and solve other issues, promoting “people’s innovation” can play a vital role. With this focus, this paper examines products produced through “people’s innovation.” A collaborative design task scheduling problem is presented. The design tasks are sorted based on a minimum delivery cost principle, which is determined using weighted shortest processing time (WSPT rules and the shortest delivery time. The results show that distributed collaborative innovation can result in a reasonable arrangement for collaborative design tasks.

  20. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. (United States)

    van Wolfswinkel, Josien C; Claycomb, Julie M; Batista, Pedro J; Mello, Craig C; Berezikov, Eugene; Ketting, René F


    We have studied the function of a conserved germline-specific nucleotidyltransferase protein, CDE-1, in RNAi and chromosome segregation in C. elegans. CDE-1 localizes specifically to mitotic chromosomes in embryos. This localization requires the RdRP EGO-1, which physically interacts with CDE-1, and the Argonaute protein CSR-1. We found that CDE-1 is required for the uridylation of CSR-1 bound siRNAs, and that in the absence of CDE-1 these siRNAs accumulate to inappropriate levels, accompanied by defects in both meiotic and mitotic chromosome segregation. Elevated siRNA levels are associated with erroneous gene silencing, most likely through the inappropriate loading of CSR-1 siRNAs into other Argonaute proteins. We propose a model in which CDE-1 restricts specific EGO-1-generated siRNAs to the CSR-1 mediated, chromosome associated RNAi pathway, thus separating it from other endogenous RNAi pathways. The conserved nature of CDE-1 suggests that similar sorting mechanisms may operate in other animals, including mammals.

  1. Digital analysis and sorting of fluorescence lifetime by flow cytometry. (United States)

    Houston, Jessica P; Naivar, Mark A; Freyer, James P


    Frequency-domain flow cytometry techniques are combined with modifications to the digital signal-processing capabilities of the open reconfigurable cytometric acquisition system (ORCAS) to analyze fluorescence decay lifetimes and control sorting. Real-time fluorescence lifetime analysis is accomplished by rapidly digitizing correlated, radiofrequency (RF)-modulated detector signals, implementing Fourier analysis programming with ORCAS' digital signal processor (DSP) and converting the processed data into standard cytometric list mode data. To systematically test the capabilities of the ORCAS 50 MS/sec analog-to-digital converter (ADC) and our DSP programming, an error analysis was performed using simulated light scatter and fluorescence waveforms (0.5-25 ns simulated lifetime), pulse widths ranging from 2 to 15 micros, and modulation frequencies from 2.5 to 16.667 MHz. The standard deviations of digitally acquired lifetime values ranged from 0.112 to >2 ns, corresponding to errors in actual phase shifts from 0.0142 degrees to 1.6 degrees. The lowest coefficients of variation (digital analysis system to a previous analog phase-sensitive flow cytometer demonstrated similar precision and accuracy on measurements of a range of fluorescent microspheres, unstained cells, and cells stained with three common fluorophores. Sorting based on fluorescence lifetime was accomplished by adding analog outputs to ORCAS and interfacing with a commercial cell sorter with a RF-modulated solid-state laser. Two populations of fluorescent microspheres with overlapping fluorescence intensities but different lifetimes (2 and 7 ns) were separated to approximately 98% purity. Overall, the digital signal acquisition and processing methods we introduce present a simple yet robust approach to phase-sensitive measurements in flow cytometry. The ability to simply and inexpensively implement this system on a commercial flow sorter will allow both better dissemination of this technology and better

  2. An Agglomeration Law for Sorting Networks and its Application in Functional Programming

    Directory of Open Access Journals (Sweden)

    Lukas Immanuel Schiller


    Full Text Available In this paper we will present a general agglomeration law for sorting networks. Agglomeration is a common technique when designing parallel programmes to control the granularity of the computation thereby finding a better fit between the algorithm and the machine on which the algorithm runs. Usually this is done by grouping smaller tasks and computing them en bloc within one parallel process. In the case of sorting networks this could be done by computing bigger parts of the network with one process. The agglomeration law in this paper pursues a different strategy: The input data is grouped and the algorithm is generalized to work on the agglomerated input while the original structure of the algorithm remains. This will result in a new access opportunity to sorting networks well-suited for efficient parallelization on modern multicore computers, computer networks or GPGPU programming. Additionally this enables us to use sorting networks as (parallel or distributed merging stages for arbitrary sorting algorithms, thereby creating new hybrid sorting algorithms with ease. The expressiveness of functional programming languages helps us to apply this law to systematically constructed sorting networks, leading to efficient and easily adaptable sorting algorithms. An application example is given, using the Eden programming language to show the effectiveness of the law. The implementation is compared with different parallel sorting algorithms by runtime behaviour.

  3. A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans. (United States)

    Romanenko, Svetlana A; Perelman, Polina L; Trifonov, Vladimir A; Serdyukova, Natalia A; Li, Tangliang; Fu, Beiyuan; O'Brien, Patricia C M; Ng, Bee L; Nie, Wenhui; Liehr, Thomas; Stanyon, Roscoe; Graphodatsky, Alexander S; Yang, Fengtang


    The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents.

  4. The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary


    Wienberg, Johannes; Jauch, Anna; Lüdecke, H J; Senger, G.; Horsthemke, B; Claussen, U.; Cremer, Thomas; Arnold, N; Lengauer, Christoph


    Fluorescencein situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescencein situ hybridization and comparative mapping of the chromosomes of ...

  5. Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome

    Directory of Open Access Journals (Sweden)

    Wen Ying


    Full Text Available Abstract Background The chromosome of Streptomyces has been shown to be unstable, frequently undergoing gross chromosomal rearrangements. However, the mechanisms underlying this phenomenon remain unclear, with previous studies focused on two chromosomal ends as targets for rearrangements. Here we investigated chromosomal instability of Streptomyces avermitilis, an important producer of avermectins, and characterized four gross chromosomal rearrangement events, including a major deletion in the central region. The present findings provide a valuable contribution to the mechanistic study of genetic instability in Streptomyces. Results Thirty randomly-selected "bald" mutants derived from the wild-type strain all contained gross chromosomal rearrangements of various types. One of the bald mutants, SA1-8, had the same linear chromosomal structure as the high avermectin-producing mutant 76-9. Chromosomes of both strains displayed at least three independent chromosomal rearrangements, including chromosomal arm replacement to form new 88-kb terminal inverted repeats (TIRs, and two major deletions. One of the deletions eliminated the 36-kb central region of the chromosome, but surprisingly did not affect viability of the cells. The other deletion (74-kb was internal to the right chromosomal arm. The chromosome of another bald mutant, SA1-6, was circularized with deletions at both ends. No obvious homology was found in all fusion sequences. Generational stability analysis showed that the chromosomal structure of SA1-8 and SA1-6 was stable. Conclusions Various chromosomal rearrangements, including chromosomal arm replacement, interstitial deletions and chromosomal circularization, occurred in S. avermitilis by non-homologous recombination. The finding of an inner deletion involving in the central region of S. avermitilis chromosome suggests that the entire Streptomyces chromosome may be the target for rearrangements, which are not limited, as previously

  6. Y-chromosome polymorphism: Possible largest Y chromosome in man?

    Energy Technology Data Exchange (ETDEWEB)

    Murthy, D.S.K.; Al-Awadi, S.A.; Bastaki, L. [Kuwait Medical Genetics Centre, Sulaibikat (Kuwait)] [and others


    The role of variations (inversions/deletion or duplication) in the heterochromatin in gonadal development and function, reproductive fitness, and malignant disease has been extensively studied. However, the causal-relationship of large Y (Yqh+) and repeated fetal loss has not been established unequivocally. An Arab couple (?Bedouin origin) with a history of repeated abortions were investigated. Karyotype analysis of the husband showed a very large Y chromosome, confirmed by GTG-, QFQ- and CBG-banding techniques. C-banding showed discontinuous distribution of the heterochromatin blocks separated by pale bands. The origin of the large heterochromatin segment could be due to tandem duplication of the Yq region or translocation (Yq:Yq). No other relatives (males) of the propositus have been available for investigation. Polymorphism of the Y chromosome could be attributed to evolutionary changes from an ancestral type, either by deletion or duplication of the heterochromatin segment. More detailed studies on isolated, aboriginal/tribal human populations will enable us to better understand the significance of the Y chromosome polymorphism.

  7. Chromosome congression explained by nanoscale electrostatics. (United States)

    Gagliardi, L John; Shain, Daniel H


    Nanoscale electrostatic microtubule disassembly forces between positively charged molecules in kinetochores and negative charges on plus ends of microtubules have been implicated in poleward chromosome motions and may also contribute to antipoleward chromosome movements. We propose that chromosome congression can be understood in terms of antipoleward nanoscale electrostatic microtubule assembly forces between negatively charged microtubule plus ends and like-charged chromosome arms, acting in conjunction with poleward microtubule disassembly forces. Several other aspects of post-attachment prometaphase chromosome motions, as well as metaphase oscillations, are consistently explained within this framework.

  8. The Chromosomes of Birds during Meiosis. (United States)

    Pigozzi, María I


    The cytological analysis of meiotic chromosomes is an exceptional tool to approach complex processes such as synapsis and recombination during the division. Chromosome studies of meiosis have been especially valuable in birds, where naturally occurring mutants or experimental knock-out animals are not available to fully investigate the basic mechanisms of major meiotic events. This review highlights the main contributions of synaptonemal complex and lampbrush chromosome research to the current knowledge of avian meiosis, with special emphasis on the organization of chromosomes during prophase I, the impact of chromosome rearrangements during meiosis, and distinctive features of the ZW pair.

  9. Polymer models of chromosome (re)organization (United States)

    Mirny, Leonid

    Chromosome Conformation Capture technique (Hi-C) provides comprehensive information about frequencies of spatial interactions between genomic loci. Inferring 3D organization of chromosomes from these data is a challenging biophysical problem. We develop a top-down approach to biophysical modeling of chromosomes. Starting with a minimal set of biologically motivated interactions we build ensembles of polymer conformations that can reproduce major features observed in Hi-C experiments. I will present our work on modeling organization of human metaphase and interphase chromosomes. Our works suggests that active processes of loop extrusion can be a universal mechanism responsible for formation of domains in interphase and chromosome compaction in metaphase.

  10. Chromosome painting of Z and W sex chromosomes in Characidium (Characiformes, Crenuchidae). (United States)

    Pazian, Marlon F; Shimabukuro-Dias, Cristiane Kioko; Pansonato-Alves, José Carlos; Oliveira, Claudio; Foresti, Fausto


    Some species of the genus Characidium have heteromorphic ZZ/ZW sex chromosomes with a totally heterochromatic W chromosome. Methods for chromosome microdissection associated with chromosome painting have become important tools for cytogenetic studies in Neotropical fish. In Characidium cf. fasciatum, the Z chromosome contains a pericentromeric heterochromatin block, whereas the W chromosome is completely heterochromatic. Therefore, a probe was produced from the W chromosome through microdissection and degenerate oligonucleotide-primed polymerase chain reaction amplification. FISH was performed using the W probe on the chromosomes of specimens of this species. This revealed expressive marks in the pericentromeric region of the Z chromosome as well as a completely painted W chromosome. When applying the same probe on chromosome preparations of C. cf. gomesi and Characidium sp., a pattern similar to C. cf. fasciatum was found, while C. cf. zebra, C. cf. lagosantense and Crenuchus spilurus species showed no hybridization signals. Structural changes in the chromosomes of an ancestral sexual system in the group that includes the species C. cf. gomesi, C. cf. fasciatum and Characidium sp., could have contributed to the process of speciation and could represent a causal mechanism of chromosomal diversification in this group. The heterochromatinization process possibly began in homomorphic and homologous chromosomes of an ancestral form, and this process could have given rise to the current patterns found in the species with sex chromosome heteromorphism.

  11. Automated multi-parametric sorting of micron-sized particles via multi-trap laser tweezers (United States)

    Kaputa, Daniel S.

    The capabilities of laser tweezers have rapidly expanded since the first demonstration by Ashkin and co-workers in 1970 of the ability to trap particles using optical energy. Laser tweezers have been used to measure piconewton forces in many biological and material science application, sort bacteria, measure DNA bond strength, and even perform microsurgery. The laser tweezers system developed for this dissertation foreshadows the next generation of laser tweezer systems that provide automated particle sorted based upon multiple criteria. Many laser tweezer sorting applications today entail the operator sorting cells from a bulk sample, one by one. This dissertation demonstrates the technologies of pattern recognition and image processing that allow for an entire microscope slide to be sorted without any operator intervention. We already live in an automated world where the cars we drive are built by machines instead of humans. The technology is there, and the only factors limiting the advancements of fully automated biological instrumentation is the lack of developers with the appropriate knowledge sets. This dissertation introduces the concept of sorting particles via a multi-parametric approach where several parameters such as size, fluorescence, and Raman spectra are used as sorting criteria. Since the advent of laser tweezers, several groups have demonstrated the ability to sort cells and other particle by size, or by fluorescence, or by any other parameter, but to our knowledge there does not exist a laser tweezer sorting system that can sort particles based upon multiple parameters. Sorting via a single parameter can be a severe limitation as the method lacks the robustness and class specificity that exists when sorting based upon multiple parameters. Simply put, it makes more sense to determine the worth of a baseball card by considering it's condition as well as it's age, rather then solely upon its condition. By adding another parameter such as the name of

  12. Chromosomal patterns in human malignant astrocytomas. (United States)

    Rey, J A; Bello, M J; de Campos, J M; Kusak, M E; Ramos, C; Benitez, J


    Cytogenetic analysis by direct and/or in vitro preparations was performed on 34 malignant astrocytomas. Thirty tumors showed near-diploid chromosome numbers, whereas, tritetraploid chromosome complements were present in four tumors. The most frequent chromosomal changes implied numerical deviations by a gain of chromosomes #7, #19, and #20, and by losses of #10, #22, and Y. Structural rearrangements were present in stem- or side lines of 24 tumors. Although no common chromosomal rearrangement seems to exist among those tumors, chromosomes #1, #6, #7, and #9 were predominantly involved. Polysomy and structural rearrangements of chromosome #7 could be related to the overexpression of epidermal growth factor gene, previously observed in some malignant gliomas.

  13. Entropy as the driver of chromosome segregation. (United States)

    Jun, Suckjoon; Wright, Andrew


    We present a new physical biology approach to understanding the relationship between the organization and segregation of bacterial chromosomes. We posit that replicated Escherichia coli daughter strands will spontaneously demix as a result of entropic forces, despite their strong confinement within the cell; in other words, we propose that entropy can act as a primordial physical force which drives chromosome segregation under the right physical conditions. Furthermore, proteins implicated in the regulation of chromosome structure and segregation may in fact function primarily in supporting such an entropy-driven segregation mechanism by regulating the physical state of chromosomes. We conclude that bacterial chromosome segregation is best understood in terms of spontaneous demixing of daughter strands. Our concept may also have important implications for chromosome segregation in eukaryotes, in which spindle-dependent chromosome movement follows an extended period of sister chromatid demixing and compaction.

  14. Flow cytometric detection of aberrant chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Gray, J.W.; Lucas, J.; Yu, L.C.; Langlois, R.


    This report describes the quantification of chromosomal aberrations by flow cytometry. Both homogeneously and heterogeneously occurring chromosome aberrations were studied. Homogeneously occurring aberrations were noted in chromosomes isolated from human colon carcinoma (LoVo) cells, stained with Hoechst 33258 and chromomycin A3 and analyzed using dual beam flow cytometry. The resulting bivariate flow karyotype showed a homogeneously occurring marker chromosome of intermediate size. Heterogeneously occurring aberrations were quantified by slit-scan flow cytometry in chromosomes isolated from control and irradiated Chinese hamster cells and stained with propidium iodide. Heterogeneously occurring dicentric chromosomes were detected by their shapes (two centrometers). The frequencies of such chromosomes estimated by slit-scan flow cytometry correlated well with the frequencies determined by visual microscopy.

  15. Chromosome X aneuploidy in Brazilian schizophrenic patients. (United States)

    de Moraes, Leopoldo Silva; Khayat, André Salim; de Lima, Patrícia Danielle Lima; Lima, Eleonidas Moura; Pinto, Giovanny Rebouças; Leal, Mariana Ferreira; de Arruda Cardoso Smith, Marília; Burbano, Rommel Rodríguez


    The identification of cytogenetic abnormalities in schizophrenic patients may provide clues to the genes involved in this disease. For this reason, a chromosomal analysis of samples from 62 schizophrenics and 70 controls was performed with trypsin-Giemsa banding and fluorescence in situ hybridization of the X chromosome. A clonal pericentric inversion on chromosome 9 was detected in one male patient, and we also discovered mosaicism associated with X chromosome aneuploidy in female patients, primarily detected in schizophrenic and normal female controls over 40 years old. When compared with age-matched female controls, the frequency of X chromosome loss was not significantly different between schizophrenics and controls, except for the 40- to 49-year-old age group. Our findings suggest that the X chromosome loss seen in schizophrenic patients is inherent to the normal cellular aging process. However, our data also suggest that X chromosome gain may be correlated with schizophrenia in this Brazilian population.

  16. Chromosomal instability determines taxane response

    DEFF Research Database (Denmark)

    Swanton, C.; Nicke, B.; Schuett, M.;


    -positive breast cancer and occurs frequently in basal-like and Her2-positive cases. In diploid cells, but not in chromosomally unstable cells, paclitaxel causes repression of CIN-survival genes, followed by cell death. In the OV01 ovarian cancer clinical trial, a high level of CIN was associated with taxane...... chromosomal instability (CIN). Silencing 22/50 of these genes, many of which are involved in DNA repair, caused cancer cell death, suggesting that these genes are involved in the survival of aneuploid cells. Overexpression of these "CIN-survival'' genes is associated with poor outcome in estrogen receptor...... resistance but carboplatin sensitivity, indicating that CIN may determine MTS response in vivo. Thus, pretherapeutic assessment of CIN may optimize treatment stratification and clinical trial design using these agents....

  17. Microdissection and chromosome painting of the alien chromosome in an addition line of wheat-Thinopyrum intermedium (United States)

    The chromosome painting is an efficient tool for chromosome research. However, plant chromosome painting is relatively underdeveloped. In this study, chromosome painting was developed and used to identify alien chromosomes in TAi-27, a wheat-Thinopyrum intermedium addition line, and chromosomes of...

  18. Bacterial Chromosome Organization and Segregation


    Toro, Esteban; Shapiro, Lucy


    Bacterial chromosomes are generally ∼1000 times longer than the cells in which they reside, and concurrent replication, segregation, and transcription/translation of this crowded mass of DNA poses a challenging organizational problem. Recent advances in cell-imaging technology with subdiffraction resolution have revealed that the bacterial nucleoid is reliably oriented and highly organized within the cell. Such organization is transmitted from one generation to the next by progressive segrega...

  19. Environmental pollution, chromosomes, and health (United States)

    Bell, Peter M.

    In mid-May, 1980, President Carter declared a state of emergency at the Love Canal area, near Niagara Falls, New York. The reason for this was for the U.S. to underwrite the relocation costs ($3-5 million) of some 2500 residents who, according to a report by the EPA (Environmental Protection Agency) may have suffered damaged chromosomes. These injuries were apparently caused by contact with toxic wastes that had been dumped in the area in the years prior to development for housing.That the toxic compounds exist in the Love Canal and Niagara Falls subsurface zones, including public water supplies, appears to be established fact. That the residents of the Love Canal area suffered chromosomal damage may be established fact as well. Whether or not these two findings can be linked to ill health of the residents is another matter. Recently, the EPA report has been described as having ‘close to zero scientific significance,’ and has been ‘discredited’(Science, 208, 123a, 1980). The reasons for this disparity go beyond differences of opinion, beyond possible inadequacies of the EPA study, and even beyond problems that probably will arise from future studies, including those now in the planning stages. The problem is that even if victims have easily recognizable injuries from toxic substances (injury that apparently has not occurred to Love Canal residents), medical science usually cannot show a causal relationship. Even chromosomal damage is, at best, difficult to interpret. In ideal studies of significant populations and control groups, the association of toxic chemical to chromosome damage and to cancer and birth defects is indirect and, up to now, has been shown to have little or no significance to an individual member of the exposed population.

  20. GSK-3 inhibitors induce chromosome instability

    Directory of Open Access Journals (Sweden)

    Staples Oliver D


    Full Text Available Abstract Background Several mechanisms operate during mitosis to ensure accurate chromosome segregation. However, during tumour evolution these mechanisms go awry resulting in chromosome instability. While several lines of evidence suggest that mutations in adenomatous polyposis coli (APC may promote chromosome instability, at least in colon cancer, the underlying mechanisms remain unclear. Here, we turn our attention to GSK-3 – a protein kinase, which in concert with APC, targets β-catenin for proteolysis – and ask whether GSK-3 is required for accurate chromosome segregation. Results To probe the role of GSK-3 in mitosis, we inhibited GSK-3 kinase activity in cells using a panel of small molecule inhibitors, including SB-415286, AR-A014418, 1-Azakenpaullone and CHIR99021. Analysis of synchronised HeLa cells shows that GSK-3 inhibitors do not prevent G1/S progression or cell division. They do, however, significantly delay mitotic exit, largely because inhibitor-treated cells have difficulty aligning all their chromosomes. Although bipolar spindles form and the majority of chromosomes biorient, one or more chromosomes often remain mono-oriented near the spindle poles. Despite a prolonged mitotic delay, anaphase frequently initiates without the last chromosome aligning, resulting in chromosome non-disjunction. To rule out the possibility of "off-target" effects, we also used RNA interference to selectively repress GSK-3β. Cells deficient for GSK-3β exhibit a similar chromosome alignment defect, with chromosomes clustered near the spindle poles. GSK-3β repression also results in cells accumulating micronuclei, a hallmark of chromosome missegregation. Conclusion Thus, not only do our observations indicate a role for GSK-3 in accurate chromosome segregation, but they also raise the possibility that, if used as therapeutic agents, GSK-3 inhibitors may induce unwanted side effects by inducing chromosome instability.

  1. Mechanisms of Chromosome Congression during Mitosis (United States)

    Maiato, Helder; Gomes, Ana Margarida; Sousa, Filipe; Barisic, Marin


    Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression. Thus, chromosome congression and maintenance of alignment are determined by different principles. Moreover, it is now clear that not all chromosomes use the same mechanism for congressing to the spindle equator. Those chromosomes that are favorably positioned between both poles when the nuclear envelope breaks down use the so-called “direct congression” pathway in which chromosomes align after bi-orientation and the establishment of end-on kinetochore-microtubule attachments. This favors the balanced action of kinetochore pulling forces and polar ejection forces along chromosome arms that drive chromosome oscillatory movements during and after congression. The other pathway, which we call “peripheral congression”, is independent of end-on kinetochore microtubule-attachments and relies on the dominant and coordinated action of the kinetochore motors Dynein and Centromere Protein E (CENP-E) that mediate the lateral transport of peripheral chromosomes along microtubules, first towards the poles and subsequently towards the equator. How the opposite polarities of kinetochore motors are regulated in space and time to drive congression of peripheral chromosomes only now starts to be understood. This appears to be regulated by position-dependent phosphorylation of both Dynein and CENP-E and by spindle microtubule

  2. Mechanisms of Chromosome Congression during Mitosis

    Directory of Open Access Journals (Sweden)

    Helder Maiato


    Full Text Available Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression. Thus, chromosome congression and maintenance of alignment are determined by different principles. Moreover, it is now clear that not all chromosomes use the same mechanism for congressing to the spindle equator. Those chromosomes that are favorably positioned between both poles when the nuclear envelope breaks down use the so-called “direct congression” pathway in which chromosomes align after bi-orientation and the establishment of end-on kinetochore-microtubule attachments. This favors the balanced action of kinetochore pulling forces and polar ejection forces along chromosome arms that drive chromosome oscillatory movements during and after congression. The other pathway, which we call “peripheral congression”, is independent of end-on kinetochore microtubule-attachments and relies on the dominant and coordinated action of the kinetochore motors Dynein and Centromere Protein E (CENP-E that mediate the lateral transport of peripheral chromosomes along microtubules, first towards the poles and subsequently towards the equator. How the opposite polarities of kinetochore motors are regulated in space and time to drive congression of peripheral chromosomes only now starts to be understood. This appears to be regulated by position-dependent phosphorylation of both Dynein and CENP-E and by spindle

  3. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Directory of Open Access Journals (Sweden)

    Sehgal Sunish K


    Full Text Available Abstract Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4% was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from

  4. Chromosome aberration assays in Allium

    Energy Technology Data Exchange (ETDEWEB)

    Grant, W.F.


    The common onion (Allium cepa) is an excellent plant for the assay of chromosome aberrations after chemical treatment. Other species of Allium (A. cepa var. proliferum, A. carinatum, A. fistulosum and A. sativum) have also been used but to a much lesser extent. Protocols have been given for using root tips from either bulbs or seeds of Allium cepa to study the cytological end-points, such as chromosome breaks and exchanges, which follow the testing of chemicals in somatic cells. It is considered that both mitotic and meiotic end-points should be used to a greater extent in assaying the cytogenetic effects of a chemical. From a literature survey, 148 chemicals are tabulated that have been assayed in 164 Allium tests for their clastogenic effect. Of the 164 assays which have been carried out, 75 are reported as giving a positive reaction, 49 positive and with a dose response, 1 positive and temperature-related, 9 borderline positive, and 30 negative; 76% of the chemicals gave a definite positive response. It is proposed that the Allium test be included among those tests routinely used for assessing chromosomal damage induced by chemicals.

  5. The Methods and Goals of Teaching Sorting Algorithms in Public Education (United States)

    Bernát, Péter


    The topic of sorting algorithms is a pleasant subject of informatics education. Not only is it so because the notion of sorting is well known from our everyday life, but also because as an algorithm task, whether we expect naive or practical solutions, it is easy to define and demonstrate. In my paper I will present some of the possible methods…

  6. A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies

    NARCIS (Netherlands)

    Reggiori, Fulvio; Pelham, Hugh R B; Reggiori, Fulvio


    Membrane proteins with transmembrane domains (TMDs) that contain polar residues exposed to the lipid bilayer are selectively sorted into multivesicular bodies (MVBs) and delivered to the yeast vacuole. Sorting of some, although not all, proteins into these structures is mediated by ubiquitination. W

  7. On the historical and conceptual background of the Wisconsin Card Sorting Test

    NARCIS (Netherlands)

    Eling, P.A.T.M.; Derckx, K.; Maes, J.H.R.


    In this paper, we describe the development of the Wisconsin Card Sorting Test (WCST). We trace the history of sorting tasks from the studies of Narziss Ach on the psychology of thinking, via the work of Kurt Goldstein and Adhemar Gelb on brain lesioned patients around 1920 and subsequent development

  8. Performance of Children with Autism Spectrum Disorders on the Dimension-Change Card Sort Task (United States)

    Dichter, Gabriel S.; Radonovich, Krestin J.; Turner-Brown, Lauren M.; Lam, Kristen S. L.; Holtzclaw, Tia N.; Bodfish, James W.


    Restricted and repetitive behaviors in autism spectrum disorders have been conceptualized to reflect impaired executive functions. In the present study, we investigated the performance of 6-17-year-old children with and without an autism spectrum disorder on a dimension-change card sort task that explicitly indicated sorting rules on every trial.…

  9. Effect of antioxidant supplementation on function and fertility of sex-sorted boar spermatozoa. (United States)

    Xia, Chunmei; Xia, Wei; Yang, Sheng; An, Lei; Li, Xihe; Wu, Zhonghong; Zhang, Jiaxing; Wang, Zhuqing; Tian, Jianhui


    The goal of this study was to investigate the effects of antioxidant supplementation on the quality of flow cytometrically-sorted boar spermatozoa. The effects of ascorbic acid-2-glucoside (AA-2G) on the sex-sorting process were evaluated using a variety of concentrations. The effects of different antioxidants (AA-2G, l-glutathione, and vitamin E) on the viability and lifespan of boar spermatozoa were also compared during sorting. Furthermore, the effect of AA-2G on acrosome intactness, the capacitation ability of sorted boar spermatozoa and pregnancy efficiency after artificial insemination (AI) at different sorting-to-insemination intervals were examined. Greater (Psperm head lateral displacement (ALH)) of the sex-sorted boar spermatozoa were greater (Pboar spermatozoa in the AA-2G-supplemented group was less (Pboar spermatozoa for the AA-2G-supplemented group were 59.25%, while the control group remains no sufficient quality semen. This study demonstrates that AA-2G supplementation can improve the quality of flow cytometrically sorted boar spermatozoa and that the optimal concentration of AA-2G for sorting is 0.068 mg/mL.

  10. Neonatal Intensive-Care Unit Graduates Show Persistent Difficulties in an Intradimensional Shift Card Sort (United States)

    Kittler, Phyllis M.; Brooks, Patricia J.; Rossi, Vanessa; Karmel, Bernard Z.; Gardner, Judith M.; Flory, Michael J.


    Neonatal intensive-care unit (NICU) graduates, a group at risk for attention problems and attention-deficit hyperactivity disorder, performed an intradimensional shift card sort at 34, 42, 51, and 60 months to assess executive function and to examine effects of individual risk factors. In the "silly" game, children sorted cards…

  11. Does Sorting Students Improve Scores? An Analysis of Class Composition. NBER Working Paper No. 18848 (United States)

    Collins, Courtney A.; Gan, Li


    This paper examines schools' decisions to sort students into different classes and how those sorting processes impact student achievement. There are two potential effects that result from schools creating homogeneous classes--a "tracking effect," which allows teachers to direct their focus to a more narrow range of students, and a peer…

  12. Advanced real-time classification methods for flow cytometry data analysis and cell sorting (United States)

    Leary, James F.; Reece, Lisa M.; Hokanson, James A.; Rosenblatt, Judah I.


    While many flow cytometric data analysis and 'discovery' methods have been developed, few of these have been applied to the problem of separating out purified cell subpopulations by cell sorting. The fundamental problem is that the data analysis techniques have been performed using relatively slow computational methods that take far more time than is allowed by the sort decision on a cell sorter (typically less than a millisecond). Thus cell sorting, which is really a form of 'real-time data classification,' is usually done with few, if any, multivariate statistical tools used either in the sort decision or in the evaluation of the correctness of the classification. We have developed new multivariate data analysis and 'data discovery' methods that can be implemented for real-time data classification for cell sorting using linked lookup tables. One multivariate 'data discovery' method, 'subtractive clustering,' has been used to find which clusters of cells are different between two or more files (cell samples) and to help guide analysis or sort boundaries for these cell subpopulations. Multivariate statistical methods (e.g. principal component analysis or discriminant function analysis) were implemented in linked lookup tables to establish analysis/sort boundaries that include 'costs (or penalties) of misclassification. Costs of misclassification provided a measure of the quality of the analysis/sort boundary and were expressed in simple terms that describe the tradeoff between yield and purity.

  13. Improved method for bacterial cell capture after flow cytometry cell sorting. (United States)

    Guillebault, D; Laghdass, M; Catala, P; Obernosterer, I; Lebaron, P


    Fixed cells with different nucleic acid contents and scatter properties (low nucleic acid [LNA], high nucleic acid 1 [HNA1], and HNA2) were sorted by flow cytometry (FCM). For each sort, 10,000 cells were efficiently captured on poly-l-lysine-coated microplates, resulting in efficient and reproducible PCR amplification.

  14. Postendocytic sorting of constitutively internalized dopamine transporter in cell lines and dopaminergic neurons

    DEFF Research Database (Denmark)

    Eriksen, Jacob; Bjørn-Yoshimoto, Walden Emil; Jørgensen, Trine Nygaard;


    The dopamine transporter (DAT) mediates reuptake of released dopamine and is the target for psychostimulants, such as cocaine and amphetamine. DAT undergoes marked constitutive endocytosis, but little is known about the fate and sorting of the endocytosed transporter. To study DAT sorting in cell...

  15. Model design and simulation of automatic sorting machine using proximity sensor

    Directory of Open Access Journals (Sweden)

    Bankole I. Oladapo


    Full Text Available The automatic sorting system has been reported to be complex and a global problem. This is because of the inability of sorting machines to incorporate flexibility in their design concept. This research therefore designed and developed an automated sorting object of a conveyor belt. The developed automated sorting machine is able to incorporate flexibility and separate species of non-ferrous metal objects and at the same time move objects automatically to the basket as defined by the regulation of the Programmable Logic Controllers (PLC with a capacitive proximity sensor to detect a value range of objects. The result obtained shows that plastic, wood, and steel were sorted into their respective and correct position with an average, sorting, time of 9.903 s, 14.072 s and 18.648 s respectively. The proposed developed model of this research could be adopted at any institution or industries, whose practices are based on mechatronics engineering systems. This is to guide the industrial sector in sorting of object and teaching aid to institutions and hence produce the list of classified materials according to the enabled sorting program commands.

  16. A Characterization of Sorting and Implications for Value-Added Estimates (United States)

    Alzen, Jessica; Domingue, Ben


    Students are non-randomly assigned, or sorted, into classrooms in various ways across and within schools. In this study, we use longitudinal data sets from three districts to investigate a metric for the characterization of sorting at the school level. We analyze whether non-random student assignment is associated with value-added estimates for…

  17. Viable cell sorting of dinoflagellates by multi-parametric flow cytometry. (United States)

    Electronic cell sorting for isolation and culture of dinoflagellates and other marine eukaryotic phytoplankton was compared to the traditional method of manually picking of cells using a micropipette. Trauma to electronically sorted cells was not a limiting factor as fragile dinoflagellates, such a...

  18. Magnetic Sorting of the Regolith on the Moon: Lunar Swirls (United States)

    Pieters, C. M.; Garrick-Bethell, I.; Hemingway, D.


    All of the mysterious albedo features on the Moon called "lunar swirls" are associated with magnetic anomalies, but not all magnetic anomalies are associated with lunar swirls [1]. It is often hypothesized that the albedo markings are tied to immature regolith on the surface, perhaps due to magnetic shielding of the solar wind and prevention of normal space weathering of the soil. Although interaction of the solar wind with the surface at swirls is indeed affected by the local magnetic field [2], this does not appear to result in immature soils on the surface. Calibrated spectra from the Moon Mineralogy Mapper [M3] (in image format) demonstrate that the high albedo markings for swirls are simply not consistent with immature regolith as is now understood from detailed analyses of lunar samples [eg 3]. However, M3 data show that the high albedo features of swirls are distinct and quite different from normal soils (in both the highlands and the mare). They allexhibit a flatter continuum across the near-infrared, but the actual band strength of ferrous minerals shows little (if any) deviation [4]. Recent analyses of magnetic field direction at swirls [5] mimic the observed albedo patterns (horizontal surface fields in bright areas, vertical surface fields in dark lanes). When coupled with the optical properties of magnetic separates of lunar soils [6] and our knowledge that the magnetic component of the soil results from space weathering [3,6], we propose a new and very simple explanation for these enigmatic albedo markings: the lunar swirls result from magnetic sorting of a well developed regolith. With time, normal gardening of the soil over a magnetic anomaly causes some of the dark magnetic component of the soil to be gradually removed from regions (high albedo areas) and accumulated in others (dark lanes). We are modeling predicted sorting rates using realistic rates of dust production. If this mechanism is tenable, only the origin of these magnetic anomalies

  19. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

    Directory of Open Access Journals (Sweden)

    Sebastian Pita


    Full Text Available In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae. The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome or both sex chromosomes (X and Y chromosomes. This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences.

  20. Whole chromosome painting of B chromosomes of the red-eye tetra Moenkhausia sanctaefilomenae (Teleostei, Characidae). (United States)

    Scudeler, Patricia Elda Sobrinho; Diniz, Débora; Wasko, Adriane Pinto; Oliveira, Claudio; Foresti, Fausto


    B chromosomes are dispensable genomic elements found in different groups of animals and plants. In the present study, a whole chromosome probe was generated from a specific heterochromatic B chromosome occurring in cells of the characidae fish Moenkhausia sanctaefilomenae (Steindachner, 1907). The chromosome painting probes were used in fluorescence in situ hybridization (FISH) experiments for the assessment of metaphase chromosomes obtained from individuals from three populations of Moenkhausia sanctaefilomenae. The results revealed that DNA sequences were shared between a specific B chromosome and many chromosomes of the A complement in all populations analyzed, suggesting a possible intra-specific origin of these B chromosomes. However, no hybridization signals were observed in other B chromosomes found in the same individuals, implying a possible independent origin of B chromosome variants in this species. FISH experiments using 18S rDNA probes revealed the presence of non-active ribosomal genes in some B chromosomes and in some chromosomes of the A complement, suggesting that at least two types of B chromosomes had an independent origin. The role of heterochromatic segments and ribosomal sequences in the origin of B chromosomes were discussed.

  1. A method for high purity sorting of rare cell subsets applied to TDC. (United States)

    Kuka, Mirela; Ashwell, Jonathan D


    T(DC) are a recently described subset of polyclonal αβ T-cells with dendritic cell properties. Because of their low number in peripheral immune compartments, isolation and characterization of T(DC) with existing purification methods are technically challenging. Here we describe a customized gating strategy and a flow cytometry-based cell sorting protocol for isolation of T(DC). The protocol was developed because, despite very conservative gating for dead-cell and doublet exclusion, cells obtained with normal sorting procedures were enriched for T(DC) but not pure. Re-sorting the output of the first round of sorting results in highly pure T(DC). Cells obtained with this method are viable and can be used for in vitro characterization. Moreover, this double-round sorting strategy can be universally applied to the isolation of other rare cell subsets.

  2. A Novel Approach to Fast Image Filtering Algorithm of Infrared Images based on Intro Sort Algorithm

    CERN Document Server

    Gupta, Kapil Kumar; Niranjan, Jitendra Kumar


    In this study we investigate the fast image filtering algorithm based on Intro sort algorithm and fast noise reduction of infrared images. Main feature of the proposed approach is that no prior knowledge of noise required. It is developed based on Stefan- Boltzmann law and the Fourier law. We also investigate the fast noise reduction approach that has advantage of less computation load. In addition, it can retain edges, details, text information even if the size of the window increases. Intro sort algorithm begins with Quick sort and switches to heap sort when the recursion depth exceeds a level based on the number of elements being sorted. This approach has the advantage of fast noise reduction by reducing the comparison time. It also significantly speed up the noise reduction process and can apply to real-time image processing. This approach will extend the Infrared images applications for medicine and video conferencing.

  3. Chromosome aberrations induced by zebularine in triticale. (United States)

    Ma, Xuhui; Wang, Qing; Wang, Yanzhi; Ma, Jieyun; Wu, Nan; Ni, Shuang; Luo, Tengxiao; Zhuang, Lifang; Chu, Chenggen; Cho, Seong-Woo; Tsujimoto, Hisashi; Qi, Zengjun


    Chromosome engineering is an important approach for generating wheat germplasm. Efficient development of chromosome aberrations will facilitate the introgression and application of alien genes in wheat. In this study, zebularine, a DNA methylation transferase inhibitor, was successfully used to induce chromosome aberrations in the octoploid triticale cultivar Jinghui#1. Dry seeds were soaked in zebularine solutions (250, 500, and 750 μmol/L) for 24 h, and the 500 μmol/L treatment was tested in three additional treatment times, i.e., 12, 36, and 48 h. All treatments induced aberrations involving wheat and rye chromosomes. Of the 920 cells observed in 67 M1 plants, 340 (37.0%) carried 817 aberrations with an average of 0.89 aberrations per cell (range: 0-12). The aberrations included probable deletions, telosomes and acentric fragments (49.0%), large segmental translocations (28.9%), small segmental translocations (17.1%), intercalary translocations (2.6%), long chromosomes that could carry more than one centromere (2.0%), and ring chromosomes (0.5%). Of 510 M2 plants analyzed, 110 (21.6%) were found to carry stable aberrations. Such aberrations included 79 with varied rye chromosome numbers, 7 with wheat and rye chromosome translocations, 15 with possible rye telosomes/deletions, and 9 with complex aberrations involving variation in rye chromosome number and wheat-rye translocations. These indicated that aberrations induced by zebularine can be steadily transmitted, suggesting that zebularine is a new efficient agent for chromosome manipulation.

  4. The importance of having two X chromosomes. (United States)

    Arnold, Arthur P; Reue, Karen; Eghbali, Mansoureh; Vilain, Eric; Chen, Xuqi; Ghahramani, Negar; Itoh, Yuichiro; Li, Jingyuan; Link, Jenny C; Ngun, Tuck; Williams-Burris, Shayna M


    Historically, it was thought that the number of X chromosomes plays little role in causing sex differences in traits. Recently, selected mouse models have been used increasingly to compare mice with the same type of gonad but with one versus two copies of the X chromosome. Study of these models demonstrates that mice with one X chromosome can be strikingly different from those with two X chromosomes, when the differences are not attributable to confounding group differences in gonadal hormones. The number of X chromosomes affects adiposity and metabolic disease, cardiovascular ischaemia/reperfusion injury and behaviour. The effects of X chromosome number are likely the result of inherent differences in expression of X genes that escape inactivation, and are therefore expressed from both X chromosomes in XX mice, resulting in a higher level of expression when two X chromosomes are present. The effects of X chromosome number contribute to sex differences in disease phenotypes, and may explain some features of X chromosome aneuploidies such as in Turner and Klinefelter syndromes.

  5. Chromosome analysis of arsenic affected cattle

    Directory of Open Access Journals (Sweden)

    S. Shekhar


    Full Text Available Aim: The aim was to study the chromosome analysis of arsenic affected cattle. Materials and Methods: 27 female cattle (21 arsenic affected and 6 normal were selected for cytogenetical study. The blood samples were collected, incubated, and cultured using appropriate media and specific methods. The samples were analyzed for chromosome number and morphology, relative length of the chromosome, arm ratio, and centromere index of X chromosome and chromosomal abnormalities in arsenic affected cattle to that of normal ones. Results: The diploid number of metaphase chromosomes in arsenic affected cattle as well as in normal cattle were all 2n=60, 58 being autosomes and 2 being sex chromosomes. From the centromeric position, karyotyping studies revealed that all the 29 pair of autosomes was found to be acrocentric or telocentric, and the sex chromosomes (XX were submetacentric in both normal and arsenic affected cattle. The relative length of all the autosome pairs and sex chrosomosome pair was found to be higher in normal than that of arsenic affected cattle. The mean arm ratio of X-chromosome was higher in normal than that of arsenic affected cattle, but it is reverse in case of centromere index value of X-chromosome. There was no significant difference of arm ratio and centromere index of X-chromosomes between arsenic affected and normal cattle. No chromosomal abnormalities were found in arsenic affected cattle. Conclusion: The chromosome analysis of arsenic affected cattle in West Bengal reported for the first time in this present study which may serve as a guideline for future studies in other species. These reference values will also help in comparison of cytological studies of arsenic affected cattle to that of various toxicants.

  6. Comparison of grape harvesting and sorting methods on factors affecting the must quality

    Directory of Open Access Journals (Sweden)

    Alessandro Parenti


    Full Text Available This study compared two harvesting techniques (manual and mechanical and three grape sorting methods (no sorting, manual, and densimetric in attempts to obtain high-quality must. The trials were carried out in 2009 and 2010 in Tuscany, Italy. The effectiveness of the harvest-sorting chain was assessed on two parameters. Substandard berries (SSB is the percentage of berries, which do not meet quality standards that enter the winemaking process, and material other than grape (MOG is a measure of the cleanliness of the berries entering the process. In the two years the trial was run the grape maturation level was widely different; in 2009 the vintage was more far mature than in 2010. With respect to SSB content and harvesting methods, in 2009 (more mature grapes hand-picking reduced SSB content, while in 2010 there were no differences between the two harvesting methods. In both years, densimetric sorting reduced SSB content, while there were no significant differences between no sorting and manual sorting. In terms of MOG content, both harvesting and sorting results were inconsistent. In 2009, MOG was lower in mechanically harvested grapes; while in 2010 it was lower in hand-picked grapes. As for sorting methods, in 2009 there were no differences in MOG, while in 2010 mechanical sorting produced better results. Our results question whether the post-harvest sorting techniques used by many estates are effective; particularly as the question has received little attention and no previous research has compared methods. Secondly, our study contributes to the debate on the effects of harvesting technique on wine quality.

  7. Discrete and continuous models of protein sorting in the Golgi (United States)

    Gong, Haijun; Schwartz, Russell


    The Golgi apparatus plays an important role in processing and sorting proteins and lipids. Golgi compartments constantly exchange material with each other and with other cellular components, allowing them to maintain and reform distinct identities despite dramatic changes in structure and size during cell division, development and osmotic stress. We have developed two minimal models of membrane and protein exchange in the Golgi --- a discrete, stochastic model [1] and a continuous ordinary differential equation (ODE) model --- both based on two fundamental mechanisms: vesicle-coat-mediated selective concentration of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins during vesicle formation and SNARE-mediated selective fusion of vesicles. Both show similar ability to establish and maintain distinct identities over broad parameter ranges, but they diverge in extreme conditions where Golgi collapse and reassembly may be observed. By exploring where the models differ, we hope to better identify those features essential to minimal models of various Golgi behaviors. [1] H. Gong, D. Sengupta, A. D. Linstedt, R. Schwartz. Biophys J. 95: 1674-1688, 2008.

  8. Novel serial positive enrichment technology enables clinical multiparameter cell sorting.

    Directory of Open Access Journals (Sweden)

    Christian Stemberger

    Full Text Available A general obstacle for clinical cell preparations is limited purity, which causes variability in the quality and potency of cell products and might be responsible for negative side effects due to unwanted contaminants. Highly pure populations can be obtained best using positive selection techniques. However, in many cases target cell populations need to be segregated from other cells by combinations of multiple markers, which is still difficult to achieve--especially for clinical cell products. Therefore, we have generated low-affinity antibody-derived Fab-fragments, which stain like parental antibodies when multimerized via Strep-tag and Strep-Tactin, but can subsequently be removed entirely from the target cell population. Such reagents can be generated for virtually any antigen and can be used for sequential positive enrichment steps via paramagnetic beads. First protocols for multiparameter enrichment of two clinically relevant cell populations, CD4(high/CD25(high/CD45RA(high 'regulatory T cells' and CD8(high/CD62L(high/CD45RA(neg 'central memory T cells', have been established to determine quality and efficacy parameters of this novel technology, which should have broad applicability for clinical cell sorting as well as basic research.

  9. Hierarchical structure of moral stages assessed by a sorting task. (United States)

    Boom, J; Brugman, D; van der Heijden, P G


    Following criticism of Kohlberg's theory of moral judgment, an empirical re-examination of hierarchical stage structure was desirable. Utilizing Piaget's concept of reflective abstraction as a basis, the hierarchical stage structure was investigated using a new method. Study participants (553 Dutch university students and 196 Russian high school students) sorted statements in terms of moral sophistication. These statements were typical for the different stages of moral development as defined in Colby and Kohlberg. The rank ordering performed by participants confirmed the hypotheses. First, despite large individual variation, the ordering of the statements that gave the best fit revealed that each consecutive Kohlbergian stage was perceived to be more morally sophisticated. Second, the lower the stage as represented by the items, the higher the agreement among the participants in their ranking; and the higher the stage as represented by the items, the lower the agreement among the participants in the rankings. Moreover, the pivotal point depended on the developmental characteristics of the sample, which demonstrated a developmental effect: The ordering of statements representative of moral stages below one's own current stage was straightforward, whereas the ordering of statements above one's own stage was difficult. It was concluded that the Piagetian idea of reflective abstraction can be used successfully to operationalize and measure the hierarchical nature of moral development.

  10. Empirical approach to interpreting card-sorting data

    Directory of Open Access Journals (Sweden)

    Steven F. Wolf1,2,*


    Full Text Available Since it was first published 30 years ago, the seminal paper of Chi et al. on expert and novice categorization of introductory problems led to a plethora of follow-up studies within and outside of the area of physics [ Cogn. Sci. 5 121 (1981]. These studies frequently encompass “card-sorting” exercises whereby the participants group problems. While this technique certainly allows insights into problem solving approaches, simple descriptive statistics more often than not fail to find significant differences between experts and novices. In moving beyond descriptive statistics, we describe a novel microscopic approach that takes into account the individual identity of the cards and uses graph theory and models to visualize, analyze, and interpret problem categorization experiments. We apply these methods to an introductory physics (mechanics problem categorization experiment, and find that most of the variation in sorting outcome is not due to the sorter being an expert versus a novice, but rather due to an independent characteristic that we named “stacker” versus “spreader.” The fact that the expert-novice distinction only accounts for a smaller amount of the variation may explain the frequent null results when conducting these experiments.

  11. Separation and sorting of cells in microsystems using physical principles (United States)

    Lee, Gi-Hun; Kim, Sung-Hwan; Ahn, Kihoon; Lee, Sang-Hoon; Park, Joong Yull


    In the last decade, microfabrication techniques have been combined with microfluidics and applied to cell biology. Utilizing such new techniques, various cell studies have been performed for the research of stem cells, immune cells, cancer, neurons, etc. Among the various biological applications of microtechnology-based platforms, cell separation technology has been highly regarded in biological and clinical fields for sorting different types of cells, finding circulating tumor cells (CTCs), and blood cell separation, amongst other things. Many cell separation methods have been created using various physical principles. Representatively, these include hydrodynamic, acoustic, dielectrophoretic, magnetic, optical, and filtering methods. In this review, each of these methods will be introduced, and their physical principles and sample applications described. Each physical principle has its own advantages and disadvantages. The engineers who design the systems and the biologists who use them should understand the pros and cons of each method or principle, to broaden the use of microsystems for cell separation. Continuous development of microsystems for cell separation will lead to new opportunities for diagnosing CTCs and cancer metastasis, as well as other elements in the bloodstream.

  12. Real-time hyperspectral processing for automatic nonferrous material sorting (United States)

    Picón, Artzai; Ghita, Ovidiu; Bereciartua, Aranzazu; Echazarra, Jone; Whelan, Paul F.; Iriondo, Pedro M.


    The application of hyperspectral sensors in the development of machine vision solutions has become increasingly popular as the spectral characteristics of the imaged materials are better modeled in the hyperspectral domain than in the standard trichromatic red, green, blue data. While there is no doubt that the availability of detailed spectral information is opportune as it opens the possibility to construct robust image descriptors, it also raises a substantial challenge when this high-dimensional data is used in the development of real-time machine vision systems. To alleviate the computational demand, often decorrelation techniques are commonly applied prior to feature extraction. While this approach has reduced to some extent the size of the spectral descriptor, data decorrelation alone proved insufficient in attaining real-time classification. This fact is particularly apparent when pixel-wise image descriptors are not sufficiently robust to model the spectral characteristics of the imaged materials, a case when the spatial information (or textural properties) also has to be included in the classification process. The integration of spectral and spatial information entails a substantial computational cost, and as a result the prospects of real-time operation for the developed machine vision system are compromised. To answer this requirement, in this paper we have reengineered the approach behind the integration of the spectral and spatial information in the material classification process to allow the real-time sorting of the nonferrous fractions that are contained in the waste of electric and electronic equipment scrap.

  13. Kinematics Card Sort Activity: Insight into Students' Thinking (United States)

    Berryhill, Erin; Herrington, Deborah; Oliver, Keith


    Kinematics is a topic students are unknowingly aware of well before entering the physics classroom. Students observe motion on a daily basis. They are constantly interpreting and making sense of their observations, unintentionally building their own understanding of kinematics before receiving any formal instruction. Unfortunately, when students take their prior conceptions to understand a new situation, they often do so in a way that inaccurately connects their learning. We were motivated to identify strategies to help our students make accurate connections to their prior knowledge and understand kinematics at a deeper level. To do this, we integrated a formative assessment card sort into a kinematic graphing unit within an introductory high school physics course. Throughout the activities, we required students to document and reflect upon their thinking. This allowed their learning to build upon their own previously held conceptual understanding, which provided an avenue for cognitive growth. By taking a more direct approach to eliciting student reasoning, we hoped to improve student learning and guide our assessment of their learning.

  14. Multiplexed labeling system for high-throughput cell sorting. (United States)

    Shin, Seung Won; Park, Kyung Soo; Song, In Hyun; Shin, Woo Jung; Kim, Byung Woo; Kim, Dong-Ik; Um, Soong Ho


    Flow cytometry and fluorescence activated cell sorting techniques were designed to realize configurable classification and separation of target cells. A number of cell phenotypes with different functionalities have recently been revealed. Before simultaneous selective capture of cells, it is desirable to label different samples with the corresponding dyes in a multiplexing manner to allow for a single analysis. However, few methods to obtain multiple fluorescent colors for various cell types have been developed. Even when restricted laser sources are employed, a small number of color codes can be expressed simultaneously. In this study, we demonstrate the ability to manifest DNA nanostructure-based multifluorescent colors formed by a complex of dyes. Highly precise self-assembly of fluorescent dye-conjugated oligonucleotides gives anisotropic DNA nanostructures, Y- and tree-shaped DNA (Y-DNA and T-DNA, respectively), which may be used as platforms for fluorescent codes. As a proof of concept, we have demonstrated seven different fluorescent codes with only two different fluorescent dyes using T-DNA. This method provides maximum efficiency for current flow cytometry. We are confident that this system will provide highly efficient multiplexed fluorescent detection for bioanalysis compared with one-to-one fluorescent correspondence for specific marker detection.

  15. Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation. (United States)

    Pandey, Ravi S; Azad, Rajeev K


    Sex chromosomes have evolved from a pair of homologous autosomes which differentiated into sex determination systems, such as XY or ZW system, as a consequence of successive recombination suppression between the gametologous chromosomes. Identifying the regions of recombination suppression, namely, the "evolutionary strata", is central to understanding the history and dynamics of sex chromosome evolution. Evolution of sex chromosomes as a consequence of serial recombination suppressions is well-studied for mammals and birds, but not for plants, although 48 dioecious plants have already been reported. Only two plants Silene latifolia and papaya have been studied until now for the presence of evolutionary strata on their X chromosomes, made possible by the sequencing of sex-linked genes on both the X and Y chromosomes, which is a requirement of all current methods that determine stratum structure based on the comparison of gametologous sex chromosomes. To circumvent this limitation and detect strata even if only the sequence of sex chromosome in the homogametic sex (i.e. X or Z chromosome) is available, we have developed an integrated segmentation and clustering method. In application to gene sequences on the papaya X chromosome and protein-coding sequences on the S. latifolia X chromosome, our method could decipher all known evolutionary strata, as reported by previous studies. Our method, after validating on known strata on the papaya and S. latifolia X chromosome, was applied to the chromosome 19 of Populus trichocarpa, an incipient sex chromosome, deciphering two, yet unknown, evolutionary strata. In addition, we applied this approach to the recently sequenced sex chromosome V of the brown alga Ectocarpus sp. that has a haploid sex determination system (UV system) recovering the sex determining and pseudoautosomal regions, and then to the mating-type chromosomes of an anther-smut fungus Microbotryum lychnidis-dioicae predicting five strata in the non

  16. Scaling Chromosomes for an Evolutionary Karyotype: A Chromosomal Tradeoff between Size and Number across Woody Species. (United States)

    Liang, Guolu; Chen, Hong


    This study aims to examine the expected scaling relationships between chromosome size and number across woody species and to clarify the importance of the scaling for the maintenance of chromosome diversity by analyzing the scaling at the inter- & intra-chromosomal level. To achieve for the goals, chromosome trait data were extracted for 191 woody species (including 56 evergreen species and 135 deciduous species) from the available literature. Cross-species analyses revealed a tradeoff among chromosomes between chromosome size and number, demonstrating there is selective mechanism crossing chromosomes among woody species. And the explanations for the result were presented from intra- to inter-chromosome contexts that the scaling may be compromises among scale symmetry, mechanical requirements, and resource allocation across chromosomes. Therein, a 3/4 scaling pattern was observed between total chromosomes and m-chromosomes within nucleus which may imply total chromosomes may evolve from more to less. In addition, the primary evolutionary trend of karyotype and the role of m-chromosomes in the process of karyotype evolution were also discussed.

  17. Microdissection and chromosome painting of X and B chromosomes in Locusta migratoria. (United States)

    Teruel, María; Cabrero, Josefa; Montiel, Eugenia E; Acosta, Manuel J; Sánchez, Antonio; Camacho, Juan Pedro M


    Acquisition of knowledge of the nature and DNA content of B chromosomes has been triggered by a collection of molecular techniques, one of which, microdissection, has provided interesting results in a number of B chromosome systems. Here we provide the first data on the molecular composition of B chromosomes in Locusta migratoria, after microdissection of the B and X chromosomes, DNA amplification by one (B) or two (X) different methods, and chromosome painting. The results showed that B chromosomes share at least two types of repetitive DNA sequences with the A chromosomes, suggesting that Bs in this species most likely arose intraspecifically. One of these repetitive DNAs is located on the heterochromatic distal half of the B chromosome and in the pericentromeric regions of about half of the A chromosomes, including the X. The other type of repetitive DNA is located interspersedly over the non-centromeric euchromatic regions of all A chromosomes and in an interstitial part of the proximal euchromatic half of the B chromosome. Chromosome painting, however, did not provide results sufficiently reliable to determine, in this species, which A chromosome gave rise to the B; this might be done by detailed analysis of the microdissected DNA sequences.

  18. Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes. (United States)

    Kitada, Kunio; Taima, Akira; Ogasawara, Kiyomoto; Metsugi, Shouichi; Aikawa, Satoko


    Analysis of structural rearrangements at the individual chromosomal level is still technologically challenging. Here we optimized a chromosome isolation method using fluorescent marker-assisted laser-capture and laser-beam microdissection and applied it to structural analysis of two aberrant chromosomes found in a lung cancer cell line. A high-density array-comparative genomic hybridization (array-CGH) analysis of DNA samples prepared from each of the chromosomes revealed that these two chromosomes contained 296 and 263 segments, respectively, ranging from 1.5 kb to 784.3 kb in size, derived from different portions of chromosome 8. Among these segments, 242 were common in both aberrant chromosomes, but 75 were found to be chromosome-specific. Sequences of 263 junction sites connecting the ends of segments were determined using a PCR/Sanger-sequencing procedure. Overlapping microhomologies were found at 169 junction sites. Junction partners came from various portions of chromosome 8 and no biased pattern in the positional distribution of junction partners was detected. These structural characteristics suggested the occurrence of random fragmentation of the entire chromosome 8 followed by random rejoining of these fragments. Based on that, we proposed a model to explain how these aberrant chromosomes are formed. Through these structural analyses, it was demonstrated that the optimized chromosome isolation method described here can provide high-quality chromosomal DNA for high resolution array-CGH analysis and probably for massively parallel sequencing analysis.


    Directory of Open Access Journals (Sweden)

    Marzieh Eskandari


    Full Text Available In the field of enterprise architecture (EA, qualitative scenarios are used to understand the qualitative characteristics better. In order to reduce the implementation cost, scenarios are prioritized to be able to focus on the higher priority and more important scenarios. There are different methods to evaluate enterprise architecture including architecture Trade-off Analysis Method (ATAM.Prioritizing qualitative scenarios is one of the main phases of this method. Since none of the recent studies meet the prioritizing qualitative scenarios requirements, considering proper prioritizing criteria and reaching an appropriate speed priority, non-dominated sorting genetic algorithms is used in this study (NSGA-II. In addition to previous research standards more criteria were considered in the proposed algorithm, these sets of structures together as gene and in the form of cell array constitute chromosome. The proposed algorithm is evaluated in two case studies in the field of enterprise architecture and architecture software. The results showed the accuracy and the more appropriate speed comparing to the previous works including genetic algorithms.

  20. Building bridges within the bacterial chromosome. (United States)

    Song, Dan; Loparo, Joseph J


    All organisms must dramatically compact their genomes to accommodate DNA within the cell. Bacteria use a set of DNA-binding proteins with low sequence specificity called nucleoid-associated proteins (NAPs) to assist in chromosome condensation and organization. By bending or bridging DNA, NAPs also facilitate chromosome segregation and regulate gene expression. Over the past decade, emerging single-molecule and chromosome conformation capture techniques have investigated the molecular mechanisms by which NAPs remodel and organize the bacterial chromosome. In this review we describe how such approaches reveal the biochemical mechanisms of three NAPs that are believed to facilitate DNA bridging: histone-like nucleoid structuring protein (H-NS), ParB, and structural maintenance of chromosomes (SMC). These three proteins form qualitatively different DNA bridges, leading to varied effects on transcription and chromosome segregation.

  1. Sexual maldevelopment and sex reversal, chromosomal causes. (United States)

    Magenis, R Ellen


    The SRY gene on the Y chromosome is the testis determining factor (TDF). It is therefore the initial male determining factor. However, phenotypic sex determination includes a cascade of genes located on autosomes as well as sex chromosomes. Aberrations of these genes may cause sexual maldevelopment or sex reversal. Abnormalities may include single gene mutations and gene loss or gain-changes may involve only sex organs or may be part of syndromes. These changes may also arise as chromosome abnormalities involving contiguous genes. Eight cases with chromosomal abnormalities involving different causative mechanisms are described herein. The most common cause is nondisjunction, including loss or gain of sex chromosomes. Less common causes are mispairing and crossing over in meiosis, chromosome breaks with repair, nonhomologous pairing due to low copy repeats and crossing over, and translocation (familial or de novo) with segregation. Cases include: [see: text].

  2. Chromosomal rearrangements in Tourette syndrome

    DEFF Research Database (Denmark)

    Bertelsen, Birgitte; Debes, Nanette Mol; Hjermind, Lena E


    Tourette syndrome (TS) is a childhood-onset complex neurobiological disorder characterized by a combination of persistent motor and vocal tics and frequent presence of other neuropsychiatric comorbidities. TS shares the fate of other complex disorders, where the genetic etiology is largely unknown......, and identification of susceptibility genes through linkage and association studies has been complicated due to inherent difficulties such as no clear mode of inheritance, genetic heterogeneity, and apparently incomplete penetrance. Positional cloning through mapping of disease-related chromosome rearrangements has...

  3. Meiosis I: When Chromosomes Undergo Extreme Makeover


    Miller, Matthew P; Amon, Angelika; Ünal, Elçin


    The ultimate success of cell division relies on the accurate partitioning of the genetic material. Errors in this process occur in nearly all tumors and are the leading cause of miscarriages and congenital birth defects in humans. Two cell divisions, mitosis and meiosis, use common as well as unique mechanisms to ensure faithful chromosome segregation. In mitosis, alternating rounds of DNA replication and chromosome segregation preserves the chromosome complement of the progenitor cell. In co...

  4. Immunophenotypic comparison of heterogenous non-sorted versus sorted mononuclear cells from human umbilical cord blood: a novel cell enrichment approach. (United States)

    Indumathi, S; Harikrishnan, R; Rajkumar, J S; Dhanasekaran, M


    Human umbilical cord blood (hUCB) has been the preferred source of stem cells for the treatment of haematological malignancies and genetic disorders. This is primarily due to its non-invasiveness, high accessibility with relative ease of isolation. Still failures do prevail due to its heterogeneity and lesser frequency of MSC identified in UCB. This study, thus, employs a cell enrichment technology to improve its therapeutic efficacy. This was achieved by immunophenotypic comparison of stem cells isolated from the heterogenous non-sorted mononuclear cells (MNCs), linage depleted (Lin+ and Lin-) fractions obtained from magnetic activated cell sorter (MACS) and sorted MNCs obtained by fluorescent activated cell sorter (FACS). The markers under consideration were CD29, CD44, CD34, CD45, CD133, CD90 and CD117. FACS sorted MNCs were rich in naive stem cell population, whereas non-sorted MNCs and lineage depleted fractions were found to be rich in progenitors. Thus, we suggest that a combination therapy of both sorted population might serve as an alternative valuable tool in treating haematologic/genetic disorders. However, further research on cell enrichment technology might give a clue for improved cell based therapy in regenerative medicine.

  5. Movement of chromosomes with severed kinetochore microtubules. (United States)

    Forer, Arthur; Johansen, Kristen M; Johansen, Jørgen


    Experiments dating from 1966 and thereafter showed that anaphase chromosomes continued to move poleward after their kinetochore microtubules were severed by ultraviolet microbeam irradiation. These observations were initially met with scepticism as they contradicted the prevailing view that kinetochore fibre microtubules pulled chromosomes to the pole. However, recent experiments using visible light laser microbeam irradiations have corroborated these earlier experiments as anaphase chromosomes again were shown to move poleward after their kinetochore microtubules were severed. Thus, multiple independent studies using different techniques have shown that chromosomes can indeed move poleward without direct microtubule connections to the pole, with only a kinetochore 'stub' of microtubules. An issue not yet settled is: what propels the disconnected chromosome? There are two not necessarily mutually exclusive proposals in the literature: (1) chromosome movement is propelled by the kinetochore stub interacting with non-kinetochore microtubules and (2) chromosome movement is propelled by a spindle matrix acting on the stub. In this review, we summarise the data indicating that chromosomes can move with severed kinetochore microtubules and we discuss proposed mechanisms for chromosome movement with severed kinetochore microtubules.

  6. Genome architecture: domain organization of interphase chromosomes. (United States)

    Bickmore, Wendy A; van Steensel, Bas


    The architecture of interphase chromosomes is important for the regulation of gene expression and genome maintenance. Chromosomes are linearly segmented into hundreds of domains with different protein compositions. Furthermore, the spatial organization of chromosomes is nonrandom and is characterized by many local and long-range contacts among genes and other sequence elements. A variety of genome-wide mapping techniques have made it possible to chart these properties at high resolution. Combined with microscopy and computational modeling, the results begin to yield a more coherent picture that integrates linear and three-dimensional (3D) views of chromosome organization in relation to gene regulation and other nuclear functions.

  7. Cognitive and medical features of chromosomal aneuploidy. (United States)

    Hutaff-Lee, Christa; Cordeiro, Lisa; Tartaglia, Nicole


    This chapter describes the physical characteristics, medical complications, and cognitive and psychological profiles that are associated with chromosomal aneuploidy conditions, a group of conditions in which individuals are born with one or more additional chromosome. Overall, chromosomal aneuploidy conditions occur in approximately 1 in 250 children. Information regarding autosomal disorders including trisomy 21 (Down syndrome), trisomy 13 (Patau syndrome), and trisomy 18 (Edward syndrome) are presented. Sex chromosome aneuploidy conditions such as Klinefelter syndrome (47,XXY), XYY, trisomy X, and Turner syndrome (45,X), in addition to less frequently occurring tetrasomy and pentasomy conditions are also covered. Treatment recommendations and suggestions for future research directions are discussed.

  8. Research on automatic human chromosome image analysis (United States)

    Ming, Delie; Tian, Jinwen; Liu, Jian


    Human chromosome karyotyping is one of the essential tasks in cytogenetics, especially in genetic syndrome diagnoses. In this thesis, an automatic procedure is introduced for human chromosome image analysis. According to different status of touching and overlapping chromosomes, several segmentation methods are proposed to achieve the best results. Medial axis is extracted by the middle point algorithm. Chromosome band is enhanced by the algorithm based on multiscale B-spline wavelets, extracted by average gray profile, gradient profile and shape profile, and calculated by the WDD (Weighted Density Distribution) descriptors. The multilayer classifier is used in classification. Experiment results demonstrate that the algorithms perform well.

  9. Meiotic chromosome abnormalities in human spermatogenesis. (United States)

    Martin, Renée H


    The last few years have witnessed an explosion in the information about chromosome abnormalities in human sperm and the meiotic events that predispose to these abnormalities. We have determined that all chromosomes are susceptible to nondisjunction, but chromosomes 21 and 22 and, especially, the sex chromosomes have an increased frequency of aneuploidy. Studies are just beginning on the effects of potential mutagens on the chromosomal constitution of human sperm. The effects of pesticides and cancer therapeutic agents have been reviewed. In the last decade, there has been a great impetus to study chromosome abnormalities in sperm from infertile men because the advent of intracytoplasmic sperm injection (ICSI) made it possible for these men to father pregnancies. A large number of studies have demonstrated that infertile men have an increased frequency of chromosomally abnormal sperm and children, even when they have a normal somatic karyotype. Meiotic studies on the pachytene stage of spermatogenesis have demonstrated that infertile men have impaired chromosome synapsis, a significantly decreased frequency of recombination, and an increased frequency of chromosomes completely lacking a recombination site. Such errors make these cells susceptible to meiotic arrest and the production of aneuploid gametes.


    Directory of Open Access Journals (Sweden)

    Linenko A. V.


    Full Text Available In the article we have considered the self-balanced potato sorting machine differing from existing designs of self-balanced potato sorting machines with an oscillatory electric drive. That drive uses a linear induction motor. As the counterbalancing device, the method of the duplicating mechanism is applied. The duplicating mechanism is a specular reflection of the main working body, and also participates in technological process. Its application in the drive of machine allows not only to increase efficiency of cleaning, drying and sorting of potatoes, but also to increase reliability of sorting installation that corresponds to the newest tendencies of development of technology. We have brought the mathematical model of the offered electric drive of potato sorting machine, which is implemented in the environment of object and visual modeling of Matlab |Simulink|. The mathematical model allows investigating influence of parameters of the linear induction electric drive on parameters of oscillatory process of working body in dynamics. The developed technique of research and the created experimental potato sorting machine with the linear induction drive have confirmed theoretical researches. The main kinematic sizes of machine and technical parameters of individual nodes are determined. It is shown, that the efficiency of inertial transportation can be increased for 20% in comparison with the classical drive from the motor of rotation. Results of research will allow to realize energetically and technologically effective potato sorting machines with the linear induction drive

  11. A cell sorting and trapping microfluidic device with an interdigital channel (United States)

    Tu, Jing; Qiao, Yi; Xu, Minghua; Li, Junji; Liang, Fupeng; Duan, Mengqin; Ju, An; Lu, Zuhong


    The growing interest in cell sorting and trapping is driving the demand for high performance technologies. Using labeling techniques or external forces, cells can be identified by a series of methods. However, all of these methods require complicated systems with expensive devices. Based on inherent differences in cellular morphology, cells can be sorted by specific structures in microfluidic devices. The weir filter is a basic and efficient cell sorting and trapping structure. However, in some existing weir devices, because of cell deformability and high flow velocity in gaps, trapped cells may become stuck or even pass through the gaps. Here, we designed and fabricated a microfluidic device with interdigital channels for cell sorting and trapping. The chip consisted of a sheet of silicone elastomer polydimethylsiloxane and a sheet of glass. A square-wave-like weir was designed in the middle of the channel, comprising the interdigital channels. The square-wave pattern extended the weir length by three times with the channel width remaining constant. Compared with a straight weir, this structure exhibited a notably higher trapping capacity. Interdigital channels provided more space to slow down the rate of the pressure decrease, which prevented the cells from becoming stuck in the gaps. Sorting a mixture K562 and blood cells to trap cells demonstrated the efficiency of the chip with the interdigital channel to sort and trap large and less deformable cells. With stable and efficient cell sorting and trapping abilities, the chip with an interdigital channel may be widely applied in scientific research fields.

  12. Sorting live stem cells based on Sox2 mRNA expression.

    Directory of Open Access Journals (Sweden)

    Hans M Larsson

    Full Text Available While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES and neural stem cells (NSC. One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+SSEA1(+ cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+ cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(- cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner.

  13. Increased chromosome radiosensitivity during pregnancy

    Energy Technology Data Exchange (ETDEWEB)

    Ricoul, Michelle; Sabatier, Laure; Dutrillaux, Bernard [Commissariat a l`Energie Atomique, Laboratoire de Radiobiologie et Oncologie, DRR, DSV, Fontenay aux roses (France)


    It was necessary to consider the risks of exposure of pregnant women, not only in relation to the child, but also in relation to their own hypersensitivity. We have demonstrated that pregnancy increases radiosensitivity of chromosome in the mouse at the end of gestation. This is of importance since it may have implications on radioprotection of pregnant women and give experimental guidelines to the problems of hypersensitivity to drugs and cancer aggravation during pregnancy. Blood obtained from women at various times of pregnancy was exposed to ionizing radiations. By comparison to non-pregnant women, an increase in chromosome breakage was observed in metaphases from lymphocytes, after short-term culture in the presence of the serum of the same donor. Immediately after delivery, this increase in radiosensitivity disappeared. In a prospective study, serial analyses showed a very strong correlation between the amount of pregnancy hormones, progesterone in particular, and the increase in radiosensitivity. Pregnant women may have an increased sensitivity to ionizing radiation during the second half of their pregnancy. This study provides the first evidence in human that radiosensitivity may vary in relation to physiological conditions.

  14. The Philadelphia chromosome in leukemogenesis

    Institute of Scientific and Technical Information of China (English)

    ZhiJieKang; JinSongYan; QuentinLiu; YuFeiLiu; LingZhiXu; ZiJieLong; DanHuang; YaYang; BingLiu; JiuXingFeng; YuJiaPan


    The truncated chromosome 22 that results from the reciprocal translocation t(9;22)(q34;q11) is known as the Phila‑delphia chromosome (Ph) and is a hallmark of chronic myeloid leukemia (CML). In leukemia cells, Ph not only impairs the physiological signaling pathways but also disrupts genomic stability. This aberrant fusion gene encodes the breakpoint cluster region‑proto‑oncogene tyrosine‑protein kinase (BCR‑ABL1) oncogenic protein with persistently enhanced tyrosine kinase activity. The kinase activity is responsible for maintaining proliferation, inhibiting differentia‑tion, and conferring resistance to cell death. During the progression of CML from the chronic phase to the accelerated phase and then to the blast phase, the expression patterns of different BCR‑ABL1 transcripts vary. Each BCR‑ABL1 transcript is present in a distinct leukemia phenotype, which predicts both response to therapy and clinical outcome. Besides CML, the Ph is found in acute lymphoblastic leukemia, acute myeloid leukemia, and mixed‑phenotype acute leukemia. Here, we provide an overview of the clinical presentation and cellular biology of different phenotypes of Ph‑positive leukemia and highlight key ifndings regarding leukemogenesis.

  15. Chromosomal replicons of higher plants

    Energy Technology Data Exchange (ETDEWEB)

    Van' t Hof, J.


    This brief discussion of replicons of higher plants offers a glimpse into the properties of chromosomal DNA replication. It gives evidence that the S phase of unrelated plant species is comprised of temporally ordered replicon families that increase in number with genome size. This orderly process, which assures a normal inheritance of genetic material to recipient daughter cells, is maintained at the level of replicon clusters by two mutually exclusive mechanisms, one involving the rate at which single replicons replicate their allotment of DNA, and another by means of the tempo-pause. The same two mechanisms are used by cells to alter the pattern of chromosomal DNA replication just prior to and during normal development. Both mechanisms are genetically determined and produce genetic effects when disturbed of disrupted by additional non-conforming DNAs. Further insight into how these two mechanisms operate requires more molecular information about the nature of replicons and the factors that govern when a replicon family replicates. Plant material is a rich and ideal source for this information just awaiting exploitation. 63 refs.

  16. Chromosomal phenotypes and submicroscopic abnormalities

    Directory of Open Access Journals (Sweden)

    Devriendt Koen


    Full Text Available Abstract The finding, during the last decade, that several common, clinically delineated syndromes are caused by submicroscopic deletions or, more rarely, by duplications, has provided a powerful tool in the annotation of the human genome. Since most microdeletion/microduplication syndromes are defined by a common deleted/duplicated region, abnormal dosage of genes located within these regions can explain the phenotypic similarities among individuals with a specific syndrome. As such, they provide a unique resource towards the genetic dissection of complex phenotypes such as congenital heart defects, mental and growth retardation and abnormal behaviour. In addition, the study of phenotypic differences in individuals with the same microdeletion syndrome may also become a treasury for the identification of modifying factors for complex phenotypes. The molecular analysis of these chromosomal anomalies has led to a growing understanding of their mechanisms of origin. Novel tools to uncover additional submicroscopic chromosomal anomalies at a higher resolution and higher speed, as well as the novel tools at hand for deciphering the modifying factors and epistatic interactors, are 'on the doorstep' and will, besides their obvious diagnostic role, play a pivotal role in the genetic dissection of complex phenotypes.

  17. Spinach seed quality - potential for combining seed size grading and chlorophyll flourescence sorting

    DEFF Research Database (Denmark)

    Deleuran, Lise Christina; Olesen, Merete Halkjær; Boelt, Birte


    might therefore improve the establishment of spinach for producers. Spinach seeds were harvested at five different times (H1, H2, H3, H4 and H5) starting 3 weeks before estimated optimum harvest time. The harvested seeds were sorted according to chlorophyll fluorescence (CF) and seed size. Two harvest.......5–3.25 mm size seeds had germinated on day 3 than both their larger and smaller counterparts at the later time of harvest (H4). Seeds with a diameter below 2.5 mm displayed the lowest MGT. Commercially, the use of chlorophyll fluorescence (CF)-sorted seeds, in combination with seed size sorting, may provide...

  18. Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform. (United States)

    Nagymihály, Zoltán; Caturello, Naidel A M S; Takátsy, Anikó; Aragay, Gemma; Kollár, László; Albuquerque, Rodrigo Q; Csók, Zsolt


    Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by (1)H or (13)C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

  19. Evaluation of a short-form of the Berg Card Sorting Test. (United States)

    Fox, Christopher J; Mueller, Shane T; Gray, Hilary M; Raber, Jacob; Piper, Brian J


    The Psychology Experimental Building Language Berg Card Sorting Test is an open-source neurobehavioral test. Participants (N = 207, ages 6 to 74) completed the Berg Card Sorting Test. Performance on the first 64 trials were isolated and compared to that on the full-length (128 trials) test. Strong correlations between the short and long forms (total errors: r = .87, perseverative response: r = .83, perseverative errors r = .77, categories completed r = .86) support the Berg Card Sorting Test-64 as an abbreviated alternative for the full-length executive function test.

  20. Immunomagnetic Indirect Positive Sorting of Precartilaginous Stem Cells from Neonatal Rat

    Institute of Scientific and Technical Information of China (English)


    To investigate the technique of sorting high-purity precartilaginous stem cells from rat's perichondrium, neonatal rat's perichondrium cells suspensions were incubated with monoclone antibody of anti-fibroblast growth factor receptor-3 (anti-FGFR-3), and the labeled cells were separated from the suspension in the magnetic field by immuno-beads coated with the second antibody. Purityof the sorted neural stem cells was found to be 93.0 %-99.0 %, with living cells amounting to 80 %-85 %. The magnetic cell sorting system could effectively separate precartilaginous stem cells fromperichondrium cell suspensions.

  1. Comparison Of Hybrid Sorting Algorithms Implemented On Different Parallel Hardware Platforms

    Directory of Open Access Journals (Sweden)

    Dominik Zurek


    Full Text Available Sorting is a common problem in computer science. There are lot of well-known sorting algorithms created for sequential execution on a single processor. Recently, hardware platforms enable to create wide parallel algorithms. We have standard processors consist of multiple cores and hardware accelerators like GPU. The graphic cards with their parallel architecture give new possibility to speed up many algorithms. In this paper we describe results of implementation of a few different sorting algorithms on GPU cards and multicore processors. Then hybrid algorithm will be presented which consists of parts executed on both platforms, standard CPU and GPU.

  2. Conservation of chromosomes syntenic with avian autosomes in squamate reptiles revealed by comparative chromosome painting. (United States)

    Pokorná, Martina; Giovannotti, Massimo; Kratochvíl, Lukáš; Caputo, Vincenzo; Olmo, Ettore; Ferguson-Smith, Malcolm A; Rens, Willem


    In contrast to mammals, birds exhibit a slow rate of chromosomal evolution. It is not clear whether high chromosome conservation is an evolutionary novelty of birds or was inherited from an earlier avian ancestor. The evolutionary conservatism of macrochromosomes between birds and turtles supports the latter possibility; however, the rate of chromosomal evolution is largely unknown in other sauropsids. In squamates, we previously reported strong conservatism of the chromosomes syntenic with the avian Z, which could reflect a peculiarity of this part of the genome. The chromosome 1 of iguanians and snakes is largely syntenic with chromosomes 3, 5 and 7 of the avian ancestral karyotype. In this project, we used comparative chromosome painting to determine how widely this synteny is conserved across nine families covering most of the main lineages of Squamata. The results suggest that the association of the avian ancestral chromosomes 3, 5 and 7 can be dated back to at least the early Jurassic and could be an ancestral characteristic for Unidentata (Serpentes, Iguania, Anguimorpha, Laterata and Scinciformata). In Squamata chromosome conservatism therefore also holds for the parts of the genome which are homologous to bird autosomes, and following on from this, a slow rate of chromosomal evolution could be a common characteristic of all sauropsids. The large evolutionary stasis in chromosome organization in birds therefore seems to be inherited from their ancestors, and it is particularly striking in comparison with mammals, probably the only major tetrapod lineage with an increased rate of chromosomal rearrangements as a whole.

  3. Card Sorting as Collaborative Method for User-Driven Information Organizing on a Website: Recommendations for Running Collaborative Group Card Sorts in Practice

    Directory of Open Access Journals (Sweden)

    Maria Friis Bjerre


    Full Text Available Card sorting is an easy-to-use, quick, inexpensive, yet powerful usability method for information organizing on a website as it generates usable input directly from end-users as to how they would expect to find information on a website. When run collaboratively in groups, the discussion between the users about the content of the cards and their relatedness provides valuable insight into the users’ mental models. Focusing on epistemic asymmetry in the group discussion, this article highlights important issues which may affect the outcome of group card sorting. It is demonstrated that group card sorting demands great attention from the test manager in relation to the composition of the group, i.e. the number of users per group and the users’ educational level and formal organizational positions, in order to ensure a result that is representative of the group as a whole.

  4. Notch Activation Is Associated with Tetraploidy and Enhanced Chromosomal Instability in Meningiomas

    Directory of Open Access Journals (Sweden)

    Gilson S. Baia


    Full Text Available The Notch signaling cascade is deregulated in diverse cancer types. Specific Notch function in cancer is dependent on the cellular context, the particular homologs expressed, and cross-talk with other signaling pathways. We have previously shown that components of the Notch signaling pathway are deregulated in meningiomas. How-ever, the functional consequence of abnormal Notch signaling to meningiomas is unknown. Here, we report that exogenous expression of the Notch pathway effector, HES1, is associated with tetraploid cells in meningioma cell lines. Activated Notch1 and Notch2 receptors induced endogenous HES1 expression and were associated with tetraploidy in meningiomas. Tetraploid meningioma cells exhibited nuclear features of chromosomal instability and increased frequency of nuclear atypia, such as multipolar mitotic spindles and accumulation of cells with large nuclei. FACS-sorted tetraploid cells are viable but have higher rates of spontaneous apoptosis when compared with diploid cells. We have used spectral karyotyping to show that, in contrast to diploid cells, tetraploid cells develop a higher number of both numerical and structural chromosomal abnormalities. Our findings identify a novel function for the Notch signaling pathway in generating tetraploidy and contributing to chromosomal instability. We speculate that abnormal Notch signaling pathway is an initiating genetic mechanism for meningioma and potentially promotes tumor development.

  5. Chromosomal painting and ZW sex chromosomes differentiation in Characidium (Characiformes, Crenuchidae

    Directory of Open Access Journals (Sweden)

    Artoni Roberto F


    Full Text Available Abstract Background The Characidium (a Neotropical fish group have a conserved diploid number (2n = 50, but show remarkable differences among species and populations in relation to sex chromosome systems and location of nucleolus organizer regions (NOR. In this study, we isolated a W-specific probe for the Characidium and characterized six Characidium species/populations using cytogenetic procedures. We analyzed the origin and differentiation of sex and NOR-bearing chromosomes by chromosome painting in populations of Characidium to reveal their evolution, phylogeny, and biogeography. Results A W-specific probe for efficient chromosome painting was isolated by microdissection and degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR amplification of W chromosomes from C. gomesi. The W probe generated weak signals dispersed on the proto sex chromosomes in C. zebra, dispersed signals in both W and Z chromosomes in C. lauroi and, in C. gomesi populations revealed a proximal site on the long arms of the Z chromosome and the entire W chromosome. All populations showed small terminal W probe sites in some autosomes. The 18S rDNA revealed distinctive patterns for each analyzed species/population with regard to proto sex chromosome, sex chromosome pair, and autosome location. Conclusions The results from dual-color fluorescence in situ hybridization (dual-color FISH using W and 18S rDNA probes allowed us to infer the putative evolutionary pathways for the differentiation of sex chromosomes and NORs, from structural rearrangements in a sex proto-chromosome, followed by gene erosion and heterochromatin amplification, morphological differentiation of the sex chromosomal pair, and NOR transposition, giving rise to the distinctive patterns observed among species/populations of Characidium. Biogeographic isolation and differentiation of sex chromosomes seem to have played a major role in the speciation process in this group of fish.

  6. Inheritance of a ring 14 chromosome. (United States)

    Riley, S B; Buckton, K E; Ratcliffe, S G; Syme, J


    A family is described in which the mother, her two live offspring, and a therapeutically aborted fetus each had a ring 14 chromosomes. The two children were mentally retarded and the mother's intelligence was at the lower end of the normal range. In addition, the mother had two spontaneous abortions, one of which was shown to be chromosomally normal.

  7. Inheritance of a ring 14 chromosome.


    Riley, S B; Buckton, K E; Ratcliffe, S G; Syme, J.


    A family is described in which the mother, her two live offspring, and a therapeutically aborted fetus each had a ring 14 chromosomes. The two children were mentally retarded and the mother's intelligence was at the lower end of the normal range. In addition, the mother had two spontaneous abortions, one of which was shown to be chromosomally normal.

  8. Human male meiotic sex chromosome inactivation

    NARCIS (Netherlands)

    Vries, M. de; Vosters, S.; Merkx, G.F.M.; Hauwers, K.W.M. d'; Wansink, D.G.; Ramos, L.; Boer, P. de


    In mammalian male gametogenesis the sex chromosomes are distinctive in both gene activity and epigenetic strategy. At first meiotic prophase the heteromorphic X and Y chromosomes are placed in a separate chromatin domain called the XY body. In this process, X,Y chromatin becomes highly phosphorylate

  9. Dynamics of chromosome segregation in Escherichia coli

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck


    Since the 1960’es the conformation and segregation of the chromosome in Escherichia coli has been a subject of interest for many scientists. However, after 40 years of research, we still know incredibly little about how the chromosome is organized inside the cell, how it manages to duplicate...

  10. Chromosome condensation: weaving an untangled web. (United States)

    Thadani, Rahul; Uhlmann, Frank


    The compaction of diffuse interphase chromatin into stable mitotic chromosomes enables the segregation of replicated DNA to daughter cells. Two new studies characterise, both in vivo and in vitro, the essential contribution of the vertebrate condensin complex to chromosome organisation.

  11. Chromosomal Aneuploidies and Early Embryonic Developmental Arrest

    Directory of Open Access Journals (Sweden)

    Maria Maurer


    Full Text Available Background: Selecting the best embryo for transfer, with the highest chance of achieving a vital pregnancy, is a major goal in current in vitro fertilization (IVF technology. The high rate of embryonic developmental arrest during IVF treatment is one of the limitations in achieving this goal. Chromosomal abnormalities are possibly linked with chromosomal arrest and selection against abnormal fertilization products. The objective of this study was to evaluate the frequency and type of chromosomal abnormalities in preimplantation embryos with developmental arrest. Materials and Methods: This cohort study included blastomeres of embryos with early developmental arrest that were biopsied and analyzed by fluorescence in-situ hybridization (FISH with probes for chromosomes 13, 16, 18, 21 and 22. Forty-five couples undergoing IVF treatment were included, and 119 arrested embryos were biopsied. All probes were obtained from the Kinderwunsch Zentrum, Linz, Austria, between August 2009 and August 2011. Results: Of these embryos, 31.6% were normal for all chromosomes tested, and 68.4% were abnormal. Eleven embryos were uniformly aneuploid, 20 were polyploid, 3 were haploid, 11 displayed mosaicism and 22 embryos exhibited chaotic chromosomal complement. Conclusion: Nearly 70% of arrested embryos exhibit chromosomal errors, making chromosomal abnormalities a major cause of embryonic arrest and may be a further explanation for the high developmental failure rates during culture of the embryos in the IVF setting.

  12. Genomic Dark Matter Illuminated: Anopheles Y Chromosomes. (United States)

    Redmond, Seth N; Neafsey, Daniel E


    Hall et al. have strategically used long-read sequencing technology to characterize the structure and highly repetitive content of the Y chromosome in Anopheles malaria mosquitoes. Their work confirms that this important but elusive heterochromatic sex chromosome is evolving extremely rapidly and harbors a remarkably small number of genes.

  13. Non-disjunction of chromosome 13

    DEFF Research Database (Denmark)

    Bugge, Merete; Collins, Andrew; Hertz, Jens Michael


    recombination in both maternal MI and MII errors and the former is associated with a significant number of tetrads (33%) that are nullichiasmate, which do not appear to be a feature of normal chromosome 13 meiosis. This study supports the evidence for subtle chromosome-specific influences on the mechanisms...

  14. Paradigm Lost: The Human Chromosome Story. (United States)

    Unger, Lawrence; Blystone, Robert V.


    Discusses whether the discovery in 1956 that humans have a chromosome number of 46, as opposed to 47 or 48 as previously thought, fits into a paradigm shift of the Kuhnian type. Concludes that Kuhn probably would not have considered the chromosome number shift to be large enough to be a focus for one of his paradigms. (AIM)

  15. Chromosome Segregation: Organizing Overlap at the Midzone

    NARCIS (Netherlands)

    Janson, M.E.; Tran, P.T.


    Sets of overlapping microtubules support the segregation of chromosomes by linking the poles of mitotic spindles. Recent work examines the effect of putting these linkages under pressure by the activation of dicentric chromosomes and sheds new light on the structural role of several well-known spind


    Institute of Scientific and Technical Information of China (English)


    Direct chromosome analysis and FISH were performed on twelve primary gastric carcinomas. Two of them had simple chromosome changes: 48,XX, +8, +20, and 49, XY, +2, +8, +9, and the others had complicated chromosome changes, which includes much more numerical and structural chromosome aberrations. Frequent structural changes in the complicated types involved chromosome 7, 3, 1, 5 and 12 etc. The del 7q was noted in eight cases. The del (3p) and del (1p) were noted in six and five cases, respectively. The results provide some important clues for isolation of the genes related to gastric cancer.

  17. Small supernumerary marker chromosomes (sSMC) in humans; are there B chromosomes hidden among them


    Ogilvie Caroline; Kosyakova Nadezda; Mrasek Kristin; Liehr Thomas; Vermeesch Joris; Trifonov Vladimir; Rubtsov Nikolai


    Abstract Background Small supernumerary marker chromosomes (sSMC) and B-chromosomes represent a heterogeneous collection of chromosomes added to the typical karyotype, and which are both small in size. They may consist of heterochromatic and/or euchromatic material. Also a predominance of maternal transmission was reported for both groups. Even though sSMC and B-chromosomes show some similarity it is still an open question if B-chromosomes are present among the heterogeneous group of sSMC. Ac...

  18. Hrs and SNX3 functions in sorting and membrane invagination within multivesicular bodies.

    Directory of Open Access Journals (Sweden)

    Véronique Pons


    Full Text Available After internalization, ubiquitinated signaling receptors are delivered to early endosomes. There, they are sorted and incorporated into the intralumenal invaginations of nascent multivesicular bodies, which function as transport intermediates to late endosomes. Receptor sorting is achieved by Hrs--an adaptor--like protein that binds membrane PtdIns3P via a FYVE motif-and then by ESCRT complexes, which presumably also mediate the invagination process. Eventually, intralumenal vesicles are delivered to lysosomes, leading to the notion that EGF receptor sorting into multivesicular bodies mediates lysosomal targeting. Here, we report that Hrs is essential for lysosomal targeting but dispensable for multivesicular body biogenesis and transport to late endosomes. By contrast, we find that the PtdIns3P-binding protein SNX3 is required for multivesicular body formation, but not for EGF receptor degradation. PtdIns3P thus controls the complementary functions of Hrs and SNX3 in sorting and multivesicular body biogenesis.

  19. Affinity-mediated sorting order reversal of single-walled carbon nanotubes in density gradient ultracentrifugation (United States)

    Jang, Myungsu; Kim, Somin; Jeong, Haneul; Ju, Sang-Yong


    Sorted single-walled carbon nanotubes (SWNTs) are of paramount importance for their utilization in high-end optoelectronic applications. Sodium cholate (SC)-based density gradient ultracentrifugation (DGU) has been instrumental in isolating small diameter (d t) SWNTs. Here, we show that SWNTs wrapped by flavin mononucleotide (FMN) as a dispersing agent are sorted in DGU, and show sorting order reversal behavior, departing from prototypical SC-SWNT trends. Larger d t SWNTs are sorted in lower density (ρ), and buoyant ρ distribution of FMN-SWNT ranges from 1.15-1.25 g cm-3. Such a nanotube layering pattern originates from both the binding affinity between FMN and SWNT and the less-susceptible hydrated volume of remote phosphate sidechains of FMN according to nanotube d t change.

  20. Binding to any ESCRT can mediate ubiquitin-independent cargo sorting (United States)

    Mageswaran, Shrawan Kumar; Dixon, Megan Gorringe; Curtiss, Matt; Keener, James P.; Babst, Markus


    The ESCRT machinery is known to sort ubiquitinated transmembrane proteins into vesicles that bud into the lumen of multivesicular bodies (MVBs). Although the ESCRTs themselves are ubiquitinated they are excluded from the intraluminal vesicles and recycle back to the cytoplasm for further rounds of sorting. To obtain insights into the rules that distinguish ESCRT machinery from cargo we analyzed the trafficking of artificial ESCRT-like protein fusions. These studies showed that lowering ESCRT-binding affinity converts a protein from behaving like ESCRT machinery into cargo of the MVB pathway, highlighting the close relationship between machinery and the cargoes they sort. Furthermore, our findings give insights into the targeting of soluble proteins into the MVB pathway and show that binding to any of the ESCRTs can mediate ubiquitin-independent MVB sorting. PMID:24148098

  1. Average-case analysis of perfect sorting by reversals (Journal Version)

    CERN Document Server

    Bouvel, Mathilde; Mishna, Marni; Rossin, Dominique


    Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. B\\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Combinatorial properties of this family of trees are essential to the algorithm analysis. Here, we use the expected value of certain tree parameters to prove that the average run-time of the algorithm is at worst, polynomial, and additionally, for sufficiently long permutations, the sorting algorithm runs in polynomial time with probability one. Furthermore, our analysis of the subclass of commuting scenarios yields precise results on the average length of a reversal, and the average number of reversals.

  2. Temporal genomic evolution of bird sex chromosomes

    DEFF Research Database (Denmark)

    Wang, Zongji; Zhang, Jilin; Yang, Wei;


    BACKGROUND: Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex...... driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS: We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous...... ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic...

  3. Advances in understanding paternally transmitted Chromosomal Abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, F; Sloter, E; Wyrobek, A J


    Multicolor FISH has been adapted for detecting the major types of chromosomal abnormalities in human sperm including aneuploidies for clinically-relevant chromosomes, chromosomal aberrations including breaks and rearrangements, and other numerical abnormalities. The various sperm FISH assays have been used to evaluate healthy men, men of advanced age, and men who have received mutagenic cancer therapy. The mouse has also been used as a model to investigate the mechanism of paternally transmitted genetic damage. Sperm FISH for the mouse has been used to detect chromosomally abnormal mouse sperm, while the PAINT/DAPI analysis of mouse zygotes has been used to evaluate the types of chromosomal defects that can be paternally transmitted to the embryo and their effects on embryonic development.

  4. Temporal genomic evolution of bird sex chromosomes

    DEFF Research Database (Denmark)

    Wang, Zongji; Zhang, Jilin; Yang, Wei;


    BACKGROUND: Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex...... driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS: We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous...... changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes...

  5. Review of the Y chromosome and hypertension

    Directory of Open Access Journals (Sweden)

    D. Ely


    Full Text Available The Y chromosome from spontaneously hypertensive rats (SHR has a locus that raises blood pressure 20-25 mmHg. Associated with the SHR Y chromosome effect is a 4-week earlier pubertal rise of testosterone and dependence upon the androgen receptor for the full blood pressure effect. Several indices of enhanced sympathetic nervous system (SNS activity are also associated with the SHR Y chromosome. Blockade of SNS outflow reduced the blood pressure effect. Salt sensitivity was increased by the Y chromosome as was salt appetite which was SNS dependent. A strong correlation (r = 0.57, P<0.001 was demonstrable between plasma testosterone and angiotensin II. Coronary collagen increased with blood pressure and the presence of the SHR Y chromosome. A promising candidate gene for the Y effect is the Sry locus (testis determining factor, a transcription factor which may also have other functions.

  6. Unusual maternal uniparental isodisomic x chromosome mosaicism with asymmetric y chromosomal rearrangement. (United States)

    Lee, B Y; Kim, S Y; Park, J Y; Choi, E Y; Kim, D J; Kim, J W; Ryu, H M; Cho, Y H; Park, S Y; Seo, J T


    Infertile men with azoospermia commonly have associated microdeletions in the azoospermia factor (AZF) region of the Y chromosome, sex chromosome mosaicism, or sex chromosome rearrangements. In this study, we describe an unusual 46,XX and 45,X mosaicism with a rare Y chromosome rearrangement in a phenotypically normal male patient. The patient's karyotype was 46,XX[50]/45,X[25]/46,X,der(Y)(pter→q11.222::p11.2→pter)[25]. The derivative Y chromosome had a deletion at Yq11.222 and was duplicated at Yp11.2. Two copies of the SRY gene were confirmed by fluorescence in situ hybridization analysis, and complete deletion of the AZFb and AZFc regions was shown by multiplex-PCR for microdeletion analysis. Both X chromosomes of the predominant mosaic cell line (46,XX) were isodisomic and derived from the maternal gamete, as determined by examination of short tandem repeat markers. We postulate that the derivative Y chromosome might have been generated during paternal meiosis or early embryogenesis. Also, we suggest that the very rare mosaicism of isodisomic X chromosomes might be formed during maternal meiosis II or during postzygotic division derived from the 46,X,der(Y)/ 45,X lineage because of the instability of the derivative Y chromosome. To our knowledge, this is the first confirmatory study to verify the origin of a sex chromosome mosaicism with a Y chromosome rearrangement.

  7. Comparative analysis by chromosome painting of the sex chromosomes in arvicolid rodents. (United States)

    Acosta, M J; Romero-Fernández, I; Sánchez, A; Marchal, J A


    Sex chromosome evolution in mammals has been extensively investigated through chromosome-painting analyses. In some rodent species from the subfamily Arvicolinae the sex chromosomes contain remarkable features such as giant size, a consequence of heterochromatic enlargement, or asynaptic behaviour during male meiosis. Here, we have made a comparative study of the sex chromosomes in 6 arvicolid species using different probes from the X and Y chromosomes of 3 species, in order to gain knowledge about intra- or interspecific preservation of euchromatic regions. Our results clearly reveal poor conservation of the euchromatic region of the Y chromosome within these species, while the euchromatin on the X chromosome is extremely well preserved. Furthermore, we detected no clear correlation between the synaptic/asynaptic behaviour of the sex chromosomes, and the presence or absence of sequence homology within their euchromatic regions. Notably, our study has shown a new relationship between the giant sex chromosomes of 2 species, Microtus agrestis and Microtus cabrerae, that is, both X and Y share a novel region of common sequences in the euchromatin that is not present in the other species analysed. This interspecific euchromatic conservation, limited to the giant sex chromosomes, could point towards a common evolutionary origin for the heterochromatic enlargement process that has characterized the evolution of the sex chromosomes in some arvicolid species.

  8. Assessing Incorrect Household Waste Sorting in a Medium-Sized Swedish City


    Kamran Rousta; Ekström, Karin M.


    Source separation is a common method for dealing with the increasing problem of Municipal Solid Waste (MSW) in society. The citizens are then responsible for separating waste fractions produced in their home. If the consumers fail to sort the waste according to the source separation scheme, it will lead to an ineffective system. The purpose of this paper is to analyze the environmental, economic and social aspects of incorrect waste sorting in a medium sized Swedish city that has established ...

  9. Photon sorting in the near field using subwavelength cavity arrays in the near-infrared

    Energy Technology Data Exchange (ETDEWEB)

    Mandel, Isroel M., E-mail:; Lansey, Eli [Department of Physics, Graduate Center and City College of the City University of New York, New York 10016 (United States); Gollub, Jonah N.; Sarantos, Chris H.; Akhmechet, Roman [Phoebus Optoelectronics, New York, New York 10013 (United States); Golovin, Andrii B.; Crouse, David T. [Department of Electrical Engineering, The City College of New York, New York, New York 10031 (United States)


    A frequency selective metasurface capable of sorting photons in the near-infrared spectral range is designed, fabricated, and characterized. The metasurface, a periodic array of dielectric cylindrical cavities in a gold film, localizes and transmits light of two spectral frequency bands into spatially separated cavities, resulting in near-field light splitting. The design and fabrication methodologies of the metasurface are discussed. The transmittance and photon sorting properties of the designed structure is simulated numerically and the measured transmission is presented.

  10. Sorted bed forms as self-organized patterns: 2. Complex forcing scenarios (United States)

    Coco, Giovanni; Murray, A. Brad; Green, Malcolm O.; Thieler, E. Robert; Hume, T. M.


    We employ a numerical model to study the development of sorted bed forms under a variety of hydrodynamic and sedimentary conditions. Results indicate that increased variability in wave height decreases the growth rate of the features and can potentially give rise to complicated, a priori unpredictable, behavior. This happens because the system responds to a change in wave characteristics by attempting to self-organize into a patterned seabed of different geometry and spacing. The new wavelength might not have enough time to emerge before a new change in wave characteristics occurs, leading to less regular seabed configurations. The new seabed configuration is also highly dependent on the preexisting morphology, which further limits the possibility of predicting future behavior. For the same reasons, variability in the mean current magnitude and direction slows down the growth of features and causes patterns to develop that differ from classical sorted bed forms. Spatial variability in grain size distribution and different types of net sediment aggradation/degradation can also result in the development of sorted bed forms characterized by a less regular shape. Numerical simulations qualitatively agree with observed geometry (spacing and height) of sorted bed forms. Also in agreement with observations is that at shallower depths, sorted bed forms are more likely to be affected by changes in the forcing conditions, which might also explain why, in shallow waters, sorted bed forms are described as ephemeral features. Finally, simulations indicate that the different sorted bed form shapes and patterns observed in the field might not necessarily be related to diverse physical mechanisms. Instead, variations in sorted bed form characteristics may result from variations in local hydrodynamic and/or sedimentary conditions.

  11. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes.

    Directory of Open Access Journals (Sweden)

    Shaun W Lim

    Full Text Available Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS. This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.

  12. Sorted bed forms as self-organized patterns: 2. complex forcing scenarios (United States)

    Coco, Giovanni; Murray, A. Brad; Green, Malcom O.; Thieler, E. Robert; Hume, T.M.


    We employ a numerical model to study the development of sorted bed forms under a variety of hydrodynamic and sedimentary conditions. Results indicate that increased variability in wave height decreases the growth rate of the features and can potentially give rise to complicated, a priori unpredictable, behavior. This happens because the system responds to a change in wave characteristics by attempting to self-organize into a patterned seabed of different geometry and spacing. The new wavelength might not have enough time to emerge before a new change in wave characteristics occurs, leading to less regular seabed configurations. The new seabed configuration is also highly dependent on the preexisting morphology, which further limits the possibility of predicting future behavior. For the same reasons, variability in the mean current magnitude and direction slows down the growth of features and causes patterns to develop that differ from classical sorted bed forms. Spatial variability in grain size distribution and different types of net sediment aggradation/degradation can also result in the development of sorted bed forms characterized by a less regular shape. Numerical simulations qualitatively agree with observed geometry (spacing and height) of sorted bed forms. Also in agreement with observations is that at shallower depths, sorted bed forms are more likely to be affected by changes in the forcing conditions, which might also explain why, in shallow waters, sorted bed forms are described as ephemeral features. Finally, simulations indicate that the different sorted bed form shapes and patterns observed in the field might not necessarily be related to diverse physical mechanisms. Instead, variations in sorted bed form characteristics may result from variations in local hydrodynamic and/or sedimentary conditions.

  13. Energy Landscapes of Folding Chromosomes (United States)

    Zhang, Bin

    The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

  14. New Y chromosomes and early stages of sex chromosome differentiation: sex determination in Megaselia

    Indian Academy of Sciences (India)

    Walther Traut


    The phorid fly Megaselia scalaris is a laboratory model for the turnover and early differentiation of sex chromosomes. Isolates from the field have an XY sex-determining mechanism with chromosome pair 2 acting as X and Y chromosomes. The sex chromosomes are homomorphic but display early signs of sex chromosome differentiation: a low level of molecular differences between X and Y. The male-determining function $(M)$, maps to the distal part of the Y chromosome’s short arm. In laboratory cultures, new Y chromosomes with no signs of a molecular differentiation arise at a low rate, probably by transposition of to these chromosomes. Downstream of the primary signal, the homologue of the Drosophila doublesex (dsx) is part of the sex-determining pathway while Sex-lethal (Sxl), though structurally conserved, is not.

  15. Novel gene acquisition on carnivore Y chromosomes.

    Directory of Open Access Journals (Sweden)

    William J Murphy


    Full Text Available Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing projects. Only the human and chimpanzee Y chromosomes have been well characterized at the sequence level. This is primarily due to the presumed low overall gene content and highly repetitive nature of the Y chromosome and the ensuing difficulties using a shotgun sequence approach for assembly. Here we used direct cDNA selection to isolate and evaluate the extent of novel Y chromosome gene acquisition in the genome of the domestic cat, a species from a different mammalian superorder than human, chimpanzee, and mouse (currently being sequenced. We discovered four novel Y chromosome genes that do not have functional copies in the finished human male-specific region of the Y or on other mammalian Y chromosomes explored thus far. Two genes are derived from putative autosomal progenitors, and the other two have X chromosome homologs from different evolutionary strata. All four genes were shown to be multicopy and expressed predominantly or exclusively in testes, suggesting that their duplication and specialization for testis function were selected for because they enhance spermatogenesis. Two of these genes have testis-expressed, Y-borne copies in the dog genome as well. The absence of the four newly described genes on other characterized mammalian Y chromosomes demonstrates the gene novelty on this chromosome between mammalian orders, suggesting it harbors many lineage-specific genes that may go undetected by traditional comparative genomic approaches. Specific plans to identify the male-specific genes encoded in the Y chromosome of mammals should be a priority.

  16. The X chromosome and immune associated genes. (United States)

    Bianchi, Ilaria; Lleo, Ana; Gershwin, M Eric; Invernizzi, Pietro


    The X chromosome is known to contain the largest number of immune-related genes of the whole human genome. For this reason, X chromosome has recently become subject of great interest and attention and numerous studies have been aimed at understanding the role of genes on the X chromosome in triggering and maintaining the autoimmune aggression. Autoimmune diseases are indeed a growing heath burden affecting cumulatively up to 10% of the general population. It is intriguing that most X-linked primary immune deficiencies carry significant autoimmune manifestations, thus illustrating the critical role played by products of single gene located on the X chromosome in the onset, function and homeostasis of the immune system. Again, the plethora of autoimmune stigmata observed in patients with Turner syndrome, a disease due to the lack of one X chromosome or the presence of major X chromosome deletions, indicate that X-linked genes play a unique and major role in autoimmunity. There have been several reports on a role of X chromosome gene dosage through inactivation or duplication in women with autoimmune diseases, for example through a higher rate of circulating cells with a single X chromosome (i.e. with X monosomy). Finally, a challenge for researchers in the coming years will be to dissect the role for the large number of X-linked microRNAs from the perspective of autoimmune disease development. Taken together, X chromosome might well constitute the common trait of the susceptibility to autoimmune diseases, other than to explain the female preponderance of these conditions. This review will focus on the available evidence on X chromosome changes and discuss their potential implications and limitations.

  17. The Role of the Clathrin Adaptor AP-1: Polarized Sorting and Beyond

    Directory of Open Access Journals (Sweden)

    Fubito Nakatsu


    Full Text Available The selective transport of proteins or lipids by vesicular transport is a fundamental process supporting cellular physiology. The budding process involves cargo sorting and vesicle formation at the donor membrane and constitutes an important process in vesicular transport. This process is particularly important for the polarized sorting in epithelial cells, in which the cargo molecules need to be selectively sorted and transported to two distinct destinations, the apical or basolateral plasma membrane. Adaptor protein (AP-1, a member of the AP complex family, which includes the ubiquitously expressed AP-1A and the epithelium-specific AP-1B, regulates polarized sorting at the trans-Golgi network and/or at the recycling endosomes. A growing body of evidence, especially from studies using model organisms and animals, demonstrates that the AP-1-mediated polarized sorting supports the development and physiology of multi-cellular units as functional organs and tissues (e.g., cell fate determination, inflammation and gut immune homeostasis. Furthermore, a possible involvement of AP-1B in the pathogenesis of human diseases, such as Crohn’s disease and cancer, is now becoming evident. These data highlight the significant contribution of AP-1 complexes to the physiology of multicellular organisms, as master regulators of polarized sorting in epithelial cells.

  18. A visual ergonomics intervention in mail sorting facilities: effects on eyes, muscles and productivity. (United States)

    Hemphälä, Hillevi; Eklund, Jörgen


    Visual requirements are high when sorting mail. The purpose of this visual ergonomics intervention study was to evaluate the visual environment in mail sorting facilities and to explore opportunities for improving the work situation by reducing visual strain, improving the visual work environment and reducing mail sorting time. Twenty-seven postmen/women participated in a pre-intervention study, which included questionnaires on their experiences of light, visual ergonomics, health, and musculoskeletal symptoms. Measurements of lighting conditions and productivity were also performed along with eye examinations of the postmen/women. The results from the pre-intervention study showed that the postmen/women who suffered from eyestrain had a higher prevalence of musculoskeletal disorders (MSD) and sorted slower, than those without eyestrain. Illuminance and illuminance uniformity improved as a result of the intervention. The two post-intervention follow-ups showed a higher prevalence of MSD among the postmen/women with eyestrain than among those without. The previous differences in sorting time for employees with and without eyestrain disappeared. After the intervention, the postmen/women felt better in general, experienced less work induced stress, and considered that the total general lighting had improved. The most pronounced decreases in eyestrain, MSD, and mail sorting time were seen among the younger participants of the group.

  19. Uncoupling the functions of CALM in VAMP sorting and clathrin-coated pit formation.

    Directory of Open Access Journals (Sweden)

    Daniela A Sahlender

    Full Text Available CALM (clathrin assembly lymphoid myeloid leukemia protein is a cargo-selective adaptor for the post-Golgi R-SNAREs VAMPs 2, 3, and 8, and it also regulates the size of clathrin-coated pits and vesicles at the plasma membrane. The present study has two objectives: to determine whether CALM can sort additional VAMPs, and to investigate whether VAMP sorting contributes to CALM-dependent vesicle size regulation. Using a flow cytometry-based endocytosis efficiency assay, we demonstrate that CALM is also able to sort VAMPs 4 and 7, even though they have sorting signals for other clathrin adaptors. CALM homologues are present in nearly every eukaryote, suggesting that the CALM family may have evolved as adaptors for retrieving all post-Golgi VAMPs from the plasma membrane. Using a knockdown/rescue system, we show that wild-type CALM restores normal VAMP sorting in CALM-depleted cells, but that two non-VAMP-binding mutants do not. However, when we assayed the effect of CALM depletion on coated pit morphology, using a fluorescence microscopy-based assay, we found that the two mutants were as effective as wild-type CALM. Thus, we can uncouple the sorting function of CALM from its structural role.

  20. Uncoupling the functions of CALM in VAMP sorting and clathrin-coated pit formation. (United States)

    Sahlender, Daniela A; Kozik, Patrycja; Miller, Sharon E; Peden, Andrew A; Robinson, Margaret S


    CALM (clathrin assembly lymphoid myeloid leukemia protein) is a cargo-selective adaptor for the post-Golgi R-SNAREs VAMPs 2, 3, and 8, and it also regulates the size of clathrin-coated pits and vesicles at the plasma membrane. The present study has two objectives: to determine whether CALM can sort additional VAMPs, and to investigate whether VAMP sorting contributes to CALM-dependent vesicle size regulation. Using a flow cytometry-based endocytosis efficiency assay, we demonstrate that CALM is also able to sort VAMPs 4 and 7, even though they have sorting signals for other clathrin adaptors. CALM homologues are present in nearly every eukaryote, suggesting that the CALM family may have evolved as adaptors for retrieving all post-Golgi VAMPs from the plasma membrane. Using a knockdown/rescue system, we show that wild-type CALM restores normal VAMP sorting in CALM-depleted cells, but that two non-VAMP-binding mutants do not. However, when we assayed the effect of CALM depletion on coated pit morphology, using a fluorescence microscopy-based assay, we found that the two mutants were as effective as wild-type CALM. Thus, we can uncouple the sorting function of CALM from its structural role.

  1. Chemokines as novel and versatile reagents for flow cytometry and cell sorting. (United States)

    Le Brocq, Michelle L; Fraser, Alasdair R; Cotton, Graham; Woznica, Kerry; McCulloch, Clare V; Hewit, Kay D; McKimmie, Clive S; Nibbs, Robert J B; Campbell, John D M; Graham, Gerard J


    Cell therapy regimens are frequently compromised by low-efficiency cell homing to therapeutic niches. Improvements in this regard would enhance effectiveness of clinically applicable cell therapy. The major regulators of tissue-specific cellular migration are chemokines, and therefore selection of therapeutic cellular populations for appropriate chemokine receptor expression would enhance tissue-homing competence. A number of practical considerations preclude the use of Abs in this context, and alternative approaches are required. In this study, we demonstrate that appropriately labeled chemokines are at least as effective in detecting their cognate receptors as commercially available Abs. We also demonstrate the utility of biotinylated chemokines as cell-sorting reagents. Specifically, we demonstrate, in the context of CCR7 (essential for lymph node homing of leukocytes), the ability of biotinylated CCL19 with magnetic bead sorting to enrich for CCR7-expressing cells. The sorted cells demonstrate improved CCR7 responsiveness and lymph node-homing capability, and the sorting is effective for both T cells and dendritic cells. Importantly, the ability of chemokines to detect CCR7, and sort for CCR7 positivity, crosses species being effective on murine and human cells. This novel approach to cell sorting is therefore inexpensive, versatile, and applicable to numerous cell therapy contexts. We propose that this represents a significant technological advance with important therapeutic implications.

  2. Differential expression of axon-sorting molecules in mouse olfactory sensory neurons. (United States)

    Ihara, Naoki; Nakashima, Ai; Hoshina, Naosuke; Ikegaya, Yuji; Takeuchi, Haruki


    In the mouse olfactory system, the axons of olfactory sensory neurons that express the same type of odorant receptor (OR) converge to a specific set of glomeruli in the olfactory bulb (OB). It is widely accepted that expressed OR molecules instruct glomerular segregation by regulating the expression of axon-sorting molecules. Although the relationship between the expression of axon-sorting molecules and OR types has been analyzed in detail, those between the expressions of axon-sorting molecules remain to be elucidated. Here we collected the expression profiles of four axon-sorting molecules from a large number of glomeruli in the OB. These molecules demonstrated position-independent mosaic expressions, but their patterns were not identical in the OB. Comparing their expressions identified positive and negative correlations between several pairs of genes even though they showed various expressions. Furthermore, the principal component analysis revealed that the factor loadings in the principal component 1, which explain the largest amount of variation, were most likely to reflect the degree of the cyclic nucleotide-gated (CNG) channel dependence on the expression of axon-sorting molecules. Thus, neural activity generated through the CNG channel is a major component in the generation of a wide variety of expressions of axon-sorting molecules in glomerular segregation.

  3. An IB-LBM study of continuous cell sorting in deterministic lateral displacement arrays (United States)

    Wei, Qiang; Xu, Yuan-Qing; Tang, Xiao-Ying; Tian, Fang-Bao


    The deterministic lateral displacement (DLD) is an important method used to sort particles and cells of different sizes. In this paper, the flexible cell sorting with the DLD method is studied by using a numerical model based on the immersed boundary-lattice Boltzmann method (IB-LBM). In this model, the fluid motion is solved by the LBM, and the cell membrane-fluid interaction is modeled with the LBM. The proposed model is validated by simulating the rigid particle sorted with the DLD method, and the results are found in good agreement with those measured in experiments. We first study the effect of flexibility on a single cell and multiple cells continuously going through a DLD device. It is found that the cell flexibility can significantly affect the cell path, which means the flexibility could have significant effects on the continuous cell sorting by the DLD method. The sorting characteristics of white blood cells and red blood cells are further studied by varying the spatial distribution of cylinder arrays and the initial cell-cell distance. The numerical results indicate that a well concentrated cell sorting can be obtained under a proper arrangement of cylinder arrays and a large enough initial cell-cell distance.

  4. Sorting out non-sorted circles: Effects of winter climate change on the Collembola community of cryoturbated subarctic tundra (United States)

    Krab, Eveline; Monteux, Sylvain; Becher, Marina; Blume-Werry, Gesche; Keuper, Frida; Klaminder, Jonatan; Kobayashi, Makoto; Lundin, Erik J.; Milbau, Ann; Roennefarth, Jonas; Teuber, Laurenz Michael; Weedon, James; Dorrepaal, Ellen


    Non-sorted circles (NSC) are a common type of cryoturbated (frost-disturbed) soil in the arctic and store large amounts of soil organic carbon (SOC) by the burial of organic matter. They appear as sparsely vegetated areas surrounded by denser tundra vegetation, creating patterned ground. Snowfall in the arctic is expected to increase, which will modify freezing intensity and freeze-thaw cycles in soils, thereby impacting on SOC dynamics. Vegetation, soil fauna and microorganisms, important drivers of carbon turnover, may benefit directly from the altered winter conditions and the resulting reduction in cryoturbation, but may also impact each other through trophic cascading. We investigated how Collembola, important decomposer soil fauna in high latitude ecosystems, are affected by increased winter insulation and vegetation cover. We subjected NSC in North-Swedish subarctic alpine tundra to two years of increased thermal insulation (snow fences or fiber cloth) in winter and spring, increasing soil temperatures and strongly reducing freeze-thaw frequency. From these NSC we sampled the Collembola community in: (i) the non-vegetated center, (ii) sparsely vegetated parts in the center and (iii) the vegetated domain surrounding NSC. To link changes in Collembola density and community composition to SOC dynamics, we included measurements of decomposer activity, dissolved organic carbon (DOC) and total extractable nitrogen (TN). We observed differences in Collembola density, community composition and soil fauna activity between the sampling points in the NSC. Specifically Collembola diversity increased with the presence of vegetation and density was higher in the vegetated outer domains. Increased winter insulation did not affect diversity but seemed to negatively affect density and decomposer activity in the vegetated outer domains. Interestingly, SOM distribution over NSC changed with snow addition (also to a lesser extent with fleece insulation) towards less SOM in the

  5. High-throughput magnetic flow sorting of human cells selected on the basis of magnetophoretic mobility (United States)

    Reece, Lisa M.; Sanders, Lehanna; Kennedy, David; Guernsey, Byron; Todd, Paul; Leary, James F.


    We have shown the potential of a new method for optimizing the separation of human stem cell subsets from peripheral blood based on a novel cell labeling technique that leverages the capabilities of a new commercially available high speed magnetic cell sorting system (IKOTECH LLC, New Albany, IN). This new system sorts cells in a continuously flowing manner using a Quadrupole Magnetic cell Sorter (QMS). The sorting mechanism is based upon the magnetophoretic mobility of the cells, a property related to the relative binding distributions of magnetic particles per cell, as determined by the utilization of a Magnetic Cell Tracking Velocimeter (MCTV). KG-1 cells were competitively labeled with anti-CD34 magnetic beads and anti-CD34 FITC to obtain an optimal level of magnetophoretic mobility as visualized by the MCTV for high throughput sort recovery in the QMS. In QMS sorting, the concept of split-flow thin channel (SPLITT) separation technology is applied by having a sample stream enter a vertical annular flow channel near the channel's interior wall followed by another sheath flow entering near the exterior wall. The two flows are initially separated by a flow splitter. They pass through the bore of a Halbach permanent quadrupole magnet assembly, which draws magnetized cells outward and deflects them into a positive outflow, while negative cells continue straight out via the inner flow lamina. QMS sorts cells based upon their magnetophoretic mobility, or the velocity of a cell per unit ponderomotive force, the counterpart of fluorescence intensity in flow cytometry. The magnetophoretic mobility distribution of a cell population, measured by automated MCTV, is used as input data for the algorithmic control of sample, sheath, and outlet flow velocities of the QMS. In this study, the relative binding distributions of magnetic particles per cell were determined by MCTV using novel sorting and sizing algorithms. The resulting mobility histograms were used to set the QMS

  6. [Y chromosome structural abnormalities and Turner's syndrome]. (United States)

    Ravel, C; Siffroi, J-P


    Although specifically male, the human Y chromosome may be observed in female karyotypes, mostly in women with Turner syndrome stigmata. In women with isolated gonadal dysgenesis but otherwise normal stature, the testis determining factor or SRY gene may have been removed from the Y chromosome or may be mutated. In other women with Turner syndrome, the karyotype is usually abnormal and shows a frequent 45,X/46,XY mosaicism. In these cases, the phenotype depends on the ratio between Y positive and 45,X cell lines in the body. When in mosaicism, Y chromosomes are likely to carry structural abnormalities which explain mitotic instability, such as the existence of two centromeres. Dicentric Y isochromosomes for the short arm (idic[Yp]) or ring Y chromosomes (r[Y]) are the most frequent abnormal Y chromosomes found in infertile patients and in Turner syndrome in mosaic with 45,X cells. Although monocentric, deleted Y chromosomes for the long arm and those carrying microdeletions in the AZF region are also instable and are frequently associated with a 45,X cell line. Management of infertile patients carrying such abnormal Y chromosomes must take into account the risk and the consequences of a mosaicism in the offspring.

  7. Developmental regulation of X-chromosome inactivation. (United States)

    Payer, Bernhard


    With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.

  8. [Dosage compensation mechanism of X chromosome]. (United States)

    Wang, Yan-Yun; Chen, Mei; Li, Bin


    Dosage compensation mechanism is crucial for the balance expression of X chromosome genes, which ensures the protein or enzyme encoded by the X chromosome to be equal or almost equal expression amounts between males and females. However, different organisms have evolved distinct dosage compensation strategies, and so far three kinds of dosage compensation strategies among organisms have been reported. The first strategy is that the single male X chromosome expression is doubly activated; the second one is to inactivate one female X chromosome by leaving both sexes with one active allele; and the third one is to reduce the expression to half activity in both X chromosomes of the female. The study of dosage compensation will be useful to reveal the mechanism of regulation of X-linked genes as well as the evolution and the differentiation progress of the sex chromosome, and it can also contribute to illustrate mutation and distortion of sex chromosome. Therefore, this paper briefly reviewed and discussed the progresses and prospects of the important mechanism of dosage compensation.

  9. Engineered human dicentric chromosomes show centromere plasticity. (United States)

    Higgins, Anne W; Gustashaw, Karen M; Willard, Huntington F


    The centromere is essential for the faithful distribution of a cell's genetic material to subsequent generations. Despite intense scrutiny, the precise genetic and epigenetic basis for centromere function is still unknown. Here, we have used engineered dicentric human chromosomes to investigate mammalian centromere structure and function. We describe three classes of dicentric chromosomes isolated in different cell lines: functionally monocentric chromosomes, in which one of the two genetically identical centromeres is consistently inactivated; functionally dicentric chromosomes, in which both centromeres are consistently active; and dicentric chromosomes heterogeneous with respect to centromere activity. A study of serial single cell clones from heterogeneous cell lines revealed that while centromere activity is usually clonal, the centromere state (i.e. functionally monocentric or dicentric) in some lines can switch within a growing population of cells. Because pulsed field gel analysis indicated that the DNA at the centromeres of these chromosomes did not change detectably, this switching of the centromere state is most likely due to epigenetic changes. Inactivation of one of the two active centromeres in a functionally dicentric chromosome was observed in a percentage of cells after treatment with Trichostatin A, an inhibitor of histone deacetylation. This study provides evidence that the activity of human centromeres, while largely stable, can be subject to dynamic change, most likely due to epigenetic modification.

  10. Chromosome I duplications in Caenorhabditis elegans

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    McKim, K.S.; Rose, A.M. (Univ. of British Columbia, Vancouver (Canada))


    We have isolated and characterized 76 duplications of chromosome I in the genome of Caenorhabditis elegans. The region studied is the 20 map unit left half of the chromosome. Sixty-two duplications were induced with gamma radiation and 14 arose spontaneously. The latter class was apparently the result of spontaneous breaks within the parental duplication. The majority of duplications behave as if they are free. Three duplications are attached to identifiable sequences from other chromosomes. The duplication breakpoints have been mapped by complementation analysis relative to genes on chromosome I. Nineteen duplication breakpoints and seven deficiency breakpoints divide the left half of the chromosome into 24 regions. We have studied the relationship between duplication size and segregational stability. While size is an important determinant of mitotic stability, it is not the only one. We observed clear exceptions to a size-stability correlation. In addition to size, duplication stability may be influenced by specific sequences or chromosome structure. The majority of the duplications were stable enough to be powerful tools for gene mapping. Therefore the duplications described here will be useful in the genetic characterization of chromosome I and the techniques we have developed can be adapted to other regions of the genome.

  11. Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data. (United States)

    Trieu, Tuan; Cheng, Jianlin


    Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene-gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as possible. We applied the objective function and the corresponding optimization method to two Hi-C chromosomal data sets of both a healthy and a cancerous human B-cell to construct 3D models of individual chromosomes at resolutions of 1 MB and 200 KB, respectively. The parameters used with the method were calibrated according to an independent fluorescence in situ hybridization experimental data. The structural models generated by our method could satisfy a high percentage of contacts (pairs of loci in interaction) and non-contacts (pairs of loci not in interaction) and were compatible with the known two-compartment organization of human chromatin structures. Furthermore, structural models generated at different resolutions and from randomly permuted data sets were consistent.

  12. Analysis of chromosome conservation in Lemur catta studied by chromosome paints and BAC/PAC probes. (United States)

    Cardone, Maria Francesca; Ventura, Mario; Tempesta, Sergio; Rocchi, Mariano; Archidiacono, Nicoletta


    A panel of human chromosome painting probes and bacterial and P1 artificial chromosome (BAC/PAC) clones were used in fluorescence in situ hybridization (FISH) experiments to investigate the chromosome conservation of the ring-tailed lemur (Lemur catta, LCA) with respect to human. Whole chromosome paints specific for human chromosomes 7, 9, 11, 13, 14, 17, 18, 20, 21, and X were found to identify a single chromosome or an uninterrupted chromosomal region in LCA. A large set of partial chromosome paints and BAC/PAC probes were then used to refine the characterization of the rearrangements differentiating the two karyotypes. The results were also used to reconstruct the ancestral Lemuridae karyotype. Lemur catta, indeed, can be used as an outgroup, allowing symplesiomorphic (ancestral) rearrangements to be distinguished from apomorphic (derived) rearrangements in lemurs. Some LCA chromosomes are difficult to distinguish morphologically. The 'anchorage' of most LCA chromosomes to specific probes will contribute to the standardization of the karyotype of this species.

  13. A cell sorting and trapping microfluidic device with an interdigital channel

    Directory of Open Access Journals (Sweden)

    Jing Tu


    Full Text Available The growing interest in cell sorting and trapping is driving the demand for high performance technologies. Using labeling techniques or external forces, cells can be identified by a series of methods. However, all of these methods require complicated systems with expensive devices. Based on inherent differences in cellular morphology, cells can be sorted by specific structures in microfluidic devices. The weir filter is a basic and efficient cell sorting and trapping structure. However, in some existing weir devices, because of cell deformability and high flow velocity in gaps, trapped cells may become stuck or even pass through the gaps. Here, we designed and fabricated a microfluidic device with interdigital channels for cell sorting and trapping. The chip consisted of a sheet of silicone elastomer polydimethylsiloxane and a sheet of glass. A square-wave-like weir was designed in the middle of the channel, comprising the interdigital channels. The square-wave pattern extended the weir length by three times with the channel width remaining constant. Compared with a straight weir, this structure exhibited a notably higher trapping capacity. Interdigital channels provided more space to slow down the rate of the pressure decrease, which prevented the cells from becoming stuck in the gaps. Sorting a mixture K562 and blood cells to trap cells demonstrated the efficiency of the chip with the interdigital channel to sort and trap large and less deformable cells. With stable and efficient cell sorting and trapping abilities, the chip with an interdigital channel may be widely applied in scientific research fields.

  14. Embryo production with sex-sorted semen in superovulated dairy heifers and cows. (United States)

    Kaimio, I; Mikkola, M; Lindeberg, H; Heikkinen, J; Hasler, J F; Taponen, J


    The aim of this study was to examine the effect of sex-sorted semen on the number and quality of embryos recovered from superovulated heifers and cows on commercial dairy farm conditions in Finland. The data consist of 1487 commercial embryo collections performed on 633 and 854 animals of Holstein and Finnish Ayrshire breeds, respectively. Superovulation was induced by eight intramuscular injections of follicle-stimulating hormone, at 12-hour intervals over 4 days, involving declining doses beginning on 9 to 12 days after the onset of standing estrus. The donors were inseminated at 9 to 15-hour intervals beginning 12 hours after the onset of estrus with 2 + 2 (+1) doses of sex-sorted frozen-thawed semen (N = 218) into the uterine horns or with 1 + 1 (+1) doses of conventional frozen-thawed semen (N = 1269) into the uterine corpus. Most conventional semen (222 bulls) straws contained 15 million sperm (total number 30-45 million per donor). Sex-sorted semen (61 bulls) straws contained 2 million sperm (total number 8-14 million per donor). Mean number of transferable embryos in recoveries from cows bred with sex-sorted semen was 4.9, which is significantly lower than 9.1 transferable embryos recovered when using conventional semen (P ≤ 0.001). In heifers, no significant difference was detected between mean number of transferable embryos in recoveries using sex-sorted semen and conventional semen (6.1 and 7.2, respectively). The number of unfertilized ova was higher when using sex-sorted semen than when using conventional semen in heifers (P cows (P cows (P protocol used seemed to be adequate for heifers. In superovulated cows, an optimal protocol for using sex-sorted semen remains to be found.

  15. Chromosomal abnormalities in patients with sperm disorders

    Directory of Open Access Journals (Sweden)

    L. Y. Pylyp


    Full Text Available Chromosomal abnormalities are among the most common genetic causes of spermatogenic disruptions. Carriers of chromosomal abnormalities are at increased risk of infertility, miscarriage or birth of a child with unbalanced karyotype due to the production of unbalanced gametes. The natural selection against chromosomally abnormal sperm usually prevents fertilization with sperm barring in cases of serious chromosomal abnormalities. However, assisted reproductive technologies in general and intracytoplasmic sperm injection in particular, enable the transmission of chromosomal abnormalities to the progeny. Therefore, cytogenetic studies are important in patients with male factor infertility before assisted reproduction treatment. The purpose of the current study was to investigate the types and frequencies of chromosomal abnormalities in 724 patients with infertility and to estimate the risk of chromosomal abnormalities detection in subgroups of patients depending on the severity of spermatogenic disruption, aiming at identifying groups of patients in need of cytogenetic studies. Karyotype analysis was performed in 724 blood samples of men attending infertility clinic. Chromosomal preparation was performed by standard techniques. At least 20 GTG-banded metaphase plates with the resolution from 450 to 750 bands per haploid set were analysed in each case. When chromosomal mosaicism was suspected, this number was increased to 50. Abnormal karyotypes were observed in 48 (6.6% patients, including 67% of autosomal abnormalities and 33% of gonosomal abnormalities. Autosomal abnormalities were represented by structural rearrangements. Reciprocal translocations were the most common type of structural chromosomal abnormalities in the studied group, detected with the frequency of 2.6% (n = 19, followed by Robertsonian translocation, observed with the frequency of 1.2% (n = 9. The frequency of inversions was 0.6% (n = 4. Gonosomal abnormalities included 14 cases

  16. Homologies between human and marmoset (Callithrix jacchus) chromosomes revealed by comparative chromosome painting

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    Sherlock, J.K.; Griffin, D.K.; Delhanty, J.D.A.; Parrington, J.M. [Univ. College London (United Kingdom)


    Regions of DNA homology between human and marmoset (Callithrix jacchus) chromosomes have been demonstrated using fluorescence in situ hybridization. All 24 chromosome paints and two centromere repeat sequences from Homo sapiens (HSA) have been annealed to previously G-banded metaphase spreads of Callithrix jacchus. All human paint probes, except Y, successfully hybridized to marmoset chromosomes. Fifteen of them hybridized to one region only, seven to two regions, and paint 1 to three regions. Homologies proposed from previous banding comparisons have been confirmed for HSA 2, 4-6, 10-12, 18, 19, 21, and X and partially confirmed for HSA 1 and 3, but were not in agreement for HSA 14 and 17. Human centromere repeat sequences for X and 18 did not hybridize to marmoset chromosomes. Because, at present, there is the confusing situation of several different numbering systems for marmoset chromosomes, we propose a new simpler nomenclature based on descending order of chromosome size. 25 refs., 3 figs.

  17. Computational modeling reveals that a combination of chemotaxis and differential adhesion leads to robust cell sorting during tissue patterning.

    Directory of Open Access Journals (Sweden)

    Rui Zhen Tan

    Full Text Available Robust tissue patterning is crucial to many processes during development. The "French Flag" model of patterning, whereby naïve cells in a gradient of diffusible morphogen signal adopt different fates due to exposure to different amounts of morphogen concentration, has been the most widely proposed model for tissue patterning. However, recently, using time-lapse experiments, cell sorting has been found to be an alternative model for tissue patterning in the zebrafish neural tube. But it remains unclear what the sorting mechanism is. In this article, we used computational modeling to show that two mechanisms, chemotaxis and differential adhesion, are needed for robust cell sorting. We assessed the performance of each of the two mechanisms by quantifying the fraction of correct sorting, the fraction of stable clusters formed after correct sorting, the time needed to achieve correct sorting, and the size variations of the cells having different fates. We found that chemotaxis and differential adhesion confer different advantages to the sorting process. Chemotaxis leads to high fraction of correct sorting as individual cells will either migrate towards or away from the source depending on its cell type. However after the cells have sorted correctly, there is no interaction among cells of the same type to stabilize the sorted boundaries, leading to cell clusters that are unstable. On the other hand, differential adhesion results in low fraction of correct clusters that are more stable. In the absence of morphogen gradient noise, a combination of both chemotaxis and differential adhesion yields cell sorting that is both accurate and robust. However, in the presence of gradient noise, the simple combination of chemotaxis and differential adhesion is insufficient for cell sorting; instead, chemotaxis coupled with delayed differential adhesion is required to yield optimal sorting.

  18. Induction and repair of DNA damage measured by the comet assay in human T lymphocytes separated by immunomagnetic cell sorting. (United States)

    Bausinger, Julia; Speit, Günter


    The comet assay is widely used in human biomonitoring to measure DNA damage in whole blood or isolated peripheral blood mononuclear cells (PBMC) as a marker of exposure to genotoxic agents. Cytogenetic assays with phytohemagglutinin (PHA)-stimulated cultured T lymphocytes are also frequently performed in human biomonitoring. Cytogenetic effects (micronuclei, chromosome aberrations, sister chromatid exchanges) may be induced in vivo but also occur ex vivo during the cultivation of lymphocytes as a consequence of DNA damage present in lymphocytes at the time of sampling. To better understand whether DNA damage measured by the comet assay in PBMC is representative for DNA damage in T cells, we comparatively investigated DNA damage and its repair in PBMC and T cells obtained by immunomagnetic cell sorting. PBMC cultures and T cell cultures were exposed to mutagens with different modes of genotoxic action and DNA damage was measured by the comet assay after the end of a 2h exposure and after 18h post-incubation. The mutagens tested were methyl methanesulfonate (MMS), (±)-anti-B[a]P-7,8-dihydrodiol-9,10-epoxide (BPDE), 4-nitroquinoline-1-oxide (4NQO), styrene oxide and potassium bromate. MMS and potassium bromate were also tested by the modified comet assay with formamido pyrimidine glycosylase (FPG) protein. The results indicate that the mutagens tested induce DNA damage in PBMC and T cells in the same range of concentrations and removal of induced DNA lesions occurs to a comparable extent. Based on these results, we conclude that the comet assay with PBMC is suited to predict DNA damage and its removal in T cells.

  19. Chromosome landmarks and autosome-sex chromosome translocations in Rumex hastatulus, a plant with XX/XY1Y2 sex chromosome system. (United States)

    Grabowska-Joachimiak, Aleksandra; Kula, Adam; Książczyk, Tomasz; Chojnicka, Joanna; Sliwinska, Elwira; Joachimiak, Andrzej J


    Rumex hastatulus is the North American endemic dioecious plant with heteromorphic sex chromosomes. It is differentiated into two chromosomal races: Texas (T) race characterised by a simple XX/XY sex chromosome system and North Carolina (NC) race with a polymorphic XX/XY1Y2 sex chromosome system. The gross karyotype morphology in NC race resembles the derived type, but chromosomal changes that occurred during its evolution are poorly understood. Our C-banding/DAPI and fluorescence in situ hybridization (FISH) experiments demonstrated that Y chromosomes of both races are enriched in DAPI-positive sequences and that the emergence of polymorphic sex chromosome system was accompanied by the break of ancestral Y chromosome and switch in the localization of 5S rDNA, from autosomes to sex chromosomes (X and Y2). Two contrasting domains were detected within North Carolina Y chromosomes: the older, highly heterochromatinised, inherited from the original Y chromosome and the younger, euchromatic, representing translocated autosomal material. The flow-cytometric DNA estimation showed ∼3.5 % genome downsizing in the North Carolina race. Our results are in contradiction to earlier reports on the lack of heterochromatin within Y chromosomes of this species and enable unambiguous identification of autosomes involved in the autosome-heterosome translocation, providing useful chromosome landmarks for further studies on the karyotype and sex chromosome differentiation in this species.

  20. Drug-induced premature chromosome condensation (PCC) protocols: cytogenetic approaches in mitotic chromosome and interphase chromatin. (United States)

    Gotoh, Eisuke


    Chromosome analysis is a fundamental technique which is used in wide areas of cytogenetic study including karyotyping species, hereditary diseases diagnosis, or chromosome biology study. Chromosomes are usually prepared from mitotic cells arrested by colcemid block protocol. However, obtaining mitotic chromosomes is often hampered under several circumstances. As a result, cytogenetic analysis will be sometimes difficult or even impossible in such cases. Premature chromosome condensation (PCC) (see Note 1) is an alternative method that has proved to be a unique and useful way in chromosome analysis. Former, PCC has been achieved following cell fusion method (cell-fusion PCC) mediated either by fusogenic viruses (e.g., Sendai virus) or cell fusion chemicals (e.g., polyethylene glycol), but the cell fusion PCC has several drawbacks. The novel drug-induced PCC using protein phosphatase inhibitors was introduced about 20 years ago. This method is much simpler and easier even than the conventional mitotic chromosome preparation protocol use with colcemid block and furthermore obtained PCC index (equivalent to mitotic index for metaphase chromosome) is usually much higher than colcemid block method. Moreover, this method allows the interphase chromatin to be condensed to visualize like mitotic chromosomes. Therefore drug-induced PCC has opened the way for chromosome analysis not only in metaphase chromosomes but also in interphase chromatin. The drug-induced PCC has thus proven the usefulness in cytogenetics and other cell biology fields. For this second edition version, updated modifications/changes are supplemented in Subheadings 2, 3, and 4, and a new section describing the application of PCC in chromosome science fields is added with citation of updated references.