bluuebunny/crossref_metadata_2025 huggingface dataset:
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
Authors: Devine Scott E. , Chissoe Stephanie L. , Eby Yolanda , Wilson Richard K. , Boeke Jef D.
Published: May 2017

Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3–140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http://www.welch.jhu.edu/~devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.

[The sequences reported in this paper have been deposited in GenBank under accession nos. U53139 and U86946–U86951.]
Microsatellite Data Support an Early Population Expansion in Africa
Authors: Shriver Mark D. , Jin Li , Ferrell Robert E. , Deka Ranjan
Published: May 2017

We have developed a method for the analysis of microsatellite data that is useful in the elucidation of the demographic history of populations. This method, the PK distribution method of pairwise comparisons, is analogous to the mismatch distribution of sequence comparisons developed for the analysis of mitochondrial sequence data by Rodgers and Harpending and is defined as the distribution of the number of repeat unit differences between alleles when each allele in a sample is compared with every other allele in the sample. Using computer simulations of microsatellite loci, we show that the shape of the distribution of PK changes in a distinctive manner as a function either of time since population expansion or effective population size. Increases in both of these affect the PK distribution in a similar fashion leading to a change from a steep distribution with a P0 peak to one with a nonzero peak. Analysis of three data sets from surveys of microsatellite loci in ethnographically defined populations reveals that most (9/12) of the African populations analyzed, but none of the 30 non-African populations showed PK distributions with nonzero peaks. These PK distributions indicate either an earlier expansion or a larger effective population size for African populations. This observation is consistent with the hypothesized African origin of modern human.
Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites
Authors: Yandava Chandri N. , Gastier Julie M. , Pulido Jacqueline C. , Brody Tom , Sheffield Val , Murray Jeffrey , Buetow Kenneth , Duyk Geoffrey M.
Published: May 2017

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containingAlu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alurepeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from ∼50% to 10%. The newAlu probes that were designed have also proved to be useful inAlu–Alu fingerprinting.
High-Resolution Mapping and Transcript Identification at the Progressive Epilepsy with Mental Retardation Locus on Chromosome 8p
Authors: Ranta Susanna , Lehesjoki Anna-Elina , Bonaldo Maria de Fatima , Knowles James A. , Hirvasniemi Aune , Ross Barbara , de Jong Pieter J. , Soares Marcelo Bento , de la Chapelle Albert , Gilliam T. Conrad
Published: May 2017

Progressive epilepsy with mental retardation (EPMR) is an autosomal recessive central nervous system disorder characterized by childhood onset epilepsy and subsequent mental retardation. The locus for EPMR has been mapped to human chromosome 8p23. We recently reported the construction of a YAC contig across the 4 centimorgan minimum genetic region that harbors the disease locus. We now report further delineation of the critical region to <700 kb. Our mapping strategy relied on the identification of nine novel microsatellite markers and the construction of a complete BAC contig across the critical region. Several partial gene sequences have been identified from the region and are being analyzed as candidate genes for EPMR.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF009188–AF009214.]
Multivariate Analysis of Factors Influencing Repeat Expansion Detection
Authors: Zander Cecilia , Thelaus Jonas , Lindblad Kerstin , Karlsson Mikael , Sjöberg Kjell , Schalling Martin
Published: May 2017

Repeat expansion detection (RED) is a powerful tool for detection of expanded repeat sequences in the genome. In RED, DNA serves as a template for a repeat-specific oligonucleotide. A thermostable ligase is used to ligate oligonucleotides that have annealed at adjacent positions, creating multimers in a thermal cycling procedure. The products are visualized after gel electrophoresis, transfered to a membrane and subsequently hybridized. Multiple linear regression (MLR) and partial least square (PLS) techniques were used to reveal the most influential factors in the amplification reaction and to identify possible interacting factors. Ligation temperature proved to be the most important factor in the reaction: Temperatures far below the melting point of the oligonucleotide increased the yield considerably. Higher cycle number resulted in a continuous rise in intensity, indicating that the ligase remained active even after 700 cycles or 12 hr of cycling. In addition, the concentration of ligase was found to be important. Using optimal parameters, a 5.5- and 3.2-fold increase in the yield of 180- and 360-nucleotide products respectively was obtained. The improved sensitivity makes the method more robust and facilitates detection of repeat expansions. This improvement may be particularly useful in development of RED for diagnostic purposes as well as for nonradioactive detection of RED products. Based on these results, a new protocol for the RED method was developed taking into account the risk of introducing artifacts with increased enzyme concentrations and lowered annealing temperatures.
Toward a Complete Human Genome Sequence
Authors: Sanger Centre The , Washington University Genome Sequencing Cente The
Published: May 2017

We have begun a joint program as part of a coordinated international effort to determine a complete human genome sequence. Our strategy is to map large-insert bacterial clones and to sequence each clone by a random shotgun approach followed by directed finishing. As of September 1998, we have identified the map positions of bacterial clones covering ∼860 Mb for sequencing and completed >98 Mb (∼3.3%) of the human genome sequence. Our progress and sequencing data can be accessed via the World Wide Web (http://webace.sanger.ac.uk/HGP/orhttp://genome.wustl.edu/gsc/).
MS205 Minisatellite Diversity in Basques: Evidence for a Pre-Neolithic Component
Authors: Alonso Santos , Armour John A.L.
Published: May 2017

A number of studies have suggested that Basques might be a relic of Mesolithic Europeans who escaped much of the homogenization brought about by the Neolithic expansion. In an attempt to add new insights into this hypothesis, MS205 minisatellite diversity has been investigated by Minisatellite Variant Repeat (MVR) analysis in a sample of >100 autochthonous individuals from the Basque Country, along with 24 Castilian (N. Spain) and 23 individuals from the United Kingdom. These populations were examined in the context of the available world database for MS205 alleles. To deduce the similarities among populations, we have applied a phylogenetic approach that takes into account similarity between alleles. The variability of these populations seems to be a subset of the greater and presumably older African diversity, as has been suggested previously for non-Africans. Within non-Africans, Basques seem to cluster with other Northern European populations; however, some apparently Basque-specific alleles can be dated back to post-Aurignacian times, supporting the continuity of some lineages of this population since the Upper Paleolithic period.
A HAPPY Map ofCryptosporidium parvum
Authors: Piper Michael B. , Bankier Alan T. , Dear Paul H.
Published: May 2017

We have constructed a HAPPY map of the apicomplexan parasiteCryptosporidium parvum. We have placed 204 markers on the 10.4-Mb genome, giving an average marker spacing of ∼50 kb, with an effective resolution of ∼40 kb. HAPPY mapping (an in vitro linkage technique based on screening approximatelyhaploid amounts of DNA by thepolymerase chain reaction) is fast and accurate and is not subject to the distortions inherent in cloning, meiotic recombination, or hybrid cell formation. In addition, little genomic DNA is needed as a substrate, and the AT content of the genome is largely immaterial, making it an ideal method for mapping otherwise intractable parasite genomes. The map, covering all eight chromosomes, consists of 10 linkage groups, each of which has been chromosomally assigned. We have verified the accuracy of the map by several methods, including the construction of a >140-kb PAC contig on chromosome VI. Less than 1% of our markers detect non-rDNA duplicated sequences.
Physical and Genetic Mapping of the Human X Chromosome Centromere: Repression of Recombination
Authors: Mahtani Melanie M. , Willard Huntington F.
Published: May 2017

Classical genetic studies in Drosophila and yeast have shown that chromosome centromeres have a cis-acting ability to repress meiotic exchange in adjacent DNA. To determine whether a similar phenomenon exists at human centromeres, we measured the rate of meiotic recombination across the centromere of the human X chromosome. We have constructed a long-range physical map of centromeric α-satellite DNA (DXZ1) by pulsed-field gel analysis, as well as detailed meiotic maps of the pericentromeric region of the X chromosome in the CEPH family panel. By comparing these two maps, we determined that, in the proximal region of the X chromosome, a genetic distance of 0.57 cM exists between markers that span the centromere and are separated by at least the average 3600 kb physical distance mapped across the DXZ1 array. Therefore, the rate of meiotic exchange across the X chromosome centromere is <1 cM/6300 kb (and perhaps as low as 1 cM/17,000 kb on the basis of other physical mapping data), at least eightfold lower than the average rate of female recombination on the X chromosome and one of the lowest rates of exchange yet observed in the human genome.
The Context of Human Genetic Evolution
Authors: Foley Robert
Published: May 2017

The debate on modern human origins has often focused on the relationship between genes and fossils. Although more and more genetic evidence has been accumulating in favor of a recent African origin for modern humans, it has been assumed by many that the fossil evidence remains ambiguous. On the contrary, it has been clear for some time that the fossil evidence does not support the multiregional model: Fossils and archeology indicate a pattern of multiple dispersals from and beyond Africa, against which the genetic data can be compared. The continuing value of paleobiology is in complementing genetic information by revealing the context of human evolution: locating the dispersals and extinctions of populations in time and space, correlating these events with the environmental forces that shaped them, and providing an increasingly detailed understanding of the morphology and technology of early humans.
Bacterial Contig Map of the 21q11 Region Associated with Alzheimer’s Disease and Abnormal Myelopoiesis in Down Syndrome
Authors: Groet Jürgen , Ives Jane H. , South Andrew P. , Baptista Pedro R. , Jones Tania A. , Yaspo Marie-Laure , Lehrach Hans , Potier Marie-Claude , Van Broeckhoven Christine , Nižetić Dean
Published: May 2017

We present a high-resolution bacterial contig map of 3.4 Mb of genomic DNA in human chromosome 21q11–q21, encompassing the region of elevated disomic homozygosity in Down Syndrome-associated abnormal myelopoiesis and leukemia, as well as the markers, which has shown a strong association with Alzheimer’s Disease that has never been explained. The map contains 89 overlapping PACs, BACs, or cosmids in three contigs (850, 850, and 1500 kb) with two gaps (one of 140–210 kb and the second <5 kb). To date, eight transcribed sequences derived by cDNA selection, exon trapping, and/or global EST sequencing have been positioned onto the map, and the only two genes so far mapped to this cytogenetic region, STCH and RIP140 have been precisely localized. This work converts a further 10% of chromosome 21q into a high-resolution bacterial contig map, which will be the physical basis for the long-range sequencing of this region. The map will also enable positional derivation of new transcribed sequences, as well as new polymorphic probes, that will help in elucidation of the role the genes in this region may play in abnormal myelopoiesis and leukemia associated with trisomy 21 and Alzheimer’s Disease.
Two Large Families of Chemoreceptor Genes in the NematodesCaenorhabditis elegans and Caenorhabditis briggsae Reveal Extensive Gene Duplication, Diversification, Movement, and Intron Loss
Authors: Robertson Hugh M.
Published: May 2017

The str family of genes encoding seven-transmembrane G-protein-coupled or serpentine receptors related to the ODR-10 diacetyl chemoreceptor is very large, with at least 197 members in theCaenorhabditis elegans genome. The closely relatedstl family has 43 genes, and both families are distantly related to the srd family with 55 genes. Analysis of the structures of these genes indicates that a third of them are clearly or likely pseudogenes. Preliminary surveys of other candidate chemoreceptor families indicates that as many as 800 genes and pseudogenes or 6% of the genome might encode 550 functional chemoreceptors constituting 4% of the C. elegans protein complement. Phylogenetic analyses of the str and stlfamilies, and comparisons with a few orthologs in Caenorhabditis briggsae, reveal ongoing processes of gene duplication, diversification, and movement. The reconstructed ancestral gene structures for these two families have eight introns each, four of which are homologous. Mapping of intron distributions on the phylogenetic tree reveals that each intron has been lost many times independently. Most of these introns were lost individually, which might best be explained by precise in-frame deletions involving nonhomologous recombination between short direct repeats at their termini.

[Alignment of the putatively functional proteins in the str and stl families is available from Pfam (http://genome.wustl.edu/Pfam); alignments of all translations are available at http://cshl.org/gr; alignments of the genes are available from the author at hughrobe@uiuc.edu]
Estimation of Distances and Map Construction Using Radiation Hybrids
Authors: Newell William , Beck Stephan , Lehrach Hans , Lyall Andrew
Published: May 2017

A method of estimating distances between pairs of genetic markers is described that directly uses their observed joint frequency distribution in a panel of radiation hybrids (RHs). The distance measure is based on the strength of association between marker pairs, which is high for close markers and decays with distance. These distances are then submitted to a previous method that generates linear coordinates for the markers directly from the intermarker distance matrix. This method of map building from RH data is simpler than others, because it uses only the observed joint frequency distributions of markers in the panel, and does not attempt to model unobserved quantities such as the retention of different sized fragments that contain the markers. It also incorporates directly the observed variation in retention of different markers, without needing a model for differential fragment retention dependent on chromosomal location, which is generally not known. Only small, precise distances are used in map construction, thereby reducing any effects of different fragment retention frequencies and local variations in X-ray sensitivity. The method is tested by simulation, and known marker distances and locations are successfully recovered from RH raw data. The method is also applied to publicly available data sets related to the recent transcript map of the human genome.
Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering
Authors: Gautheret Daniel , Poirot Olivier , Lopez Fabrice , Audic Stéphane , Claverie Jean-Michel
Published: May 2017

Alternate polyadenylation is an important post-transcriptional regulatory process now open to large-scale analysis by use of cDNA databases. We clustered 164,000 expressed sequence tags (ESTs) into ∼15,000 groups and aligned each group to a putative mRNA 3′ end. By use of stringent criteria to discard artifactual mRNA extremities, clear evidence for alternate polyadenylation was obtained in 189 of the 1000 EST clusters studied. A number of previously unreported polyadenylation sites were identified, together with possible instances of tissue-specific differential polyadenylation. This study demonstrates that, besides quantitative aspects of gene expression, the distribution of alternate mRNA forms can be analyzed through EST sampling.
A High-Resolution Microsatellite Map of the Mouse Genome
Authors: Rhodes Michael , Straw Richard , Fernando Supem , Evans Andrew , Lacey Tregaye , Dearlove Andrew , Greystrong John , Walker Joanne , Watson Paula , Weston Paul , Kelly Maria , Taylor Dilip , Gibson Keith , Mundy Chris , Bourgade Franck , Poirier Christophe , Simon Dominique , Brunialti Ana Lucia Bueno , Montagutelli Xavier , Gu′enet Jean-Louis , Haynes Andy , Brown Steve D.M.
Published: May 2017

The European Collaborative Interspecific Backcross (EUCIB) resource was constructed for the purposes of high-resolution genetic mapping of the mouse genome (Breen et al. 1994). The large Mus spretus/C57BL/6 backcross of 982 progeny has a genetic resolution of 0.3 cM at the 95% confidence level (∼500 kb in the mouse genome). We have used the EUCIB mapping resource to develop a genome-wide high-resolution genetic map incorporating 3368 microsatellites. The microsatellites are distributed among 2302 genetically separated bins with 1.46 markers per bin on average. Average bin separation is 0.61 cM. This high-resolution genetic map will aid the construction of a robust physical map of the mouse genome.
Ribonuclease k6: Chromosomal Mapping and Divergent Rates of Evolution within the RNase A Gene Superfamily
Authors: Deming Madeleine S. , Dyer Kimberly D. , Bankier Alan T. , Piper Michael B. , Dear Paul H. , Rosenberg Helene F.
Published: May 2017

We have localized the gene encoding human RNase k6 to within ∼120 kb on the long (q) arm of chromosome 14 by HAPPY mapping. With this information, the relative positions of the six human RNase A ribonucleases that have been mapped to this locus can be inferred. To further our understanding of the individual lineages comprising the RNase A superfamily, we have isolated and characterized 10 novel genes orthologous to that encoding human RNase k6 from Great Ape, Old World, and New World monkey genomes. Each gene encodes a complete ORF with no less than 86% amino acid sequence identity to human RNase k6 with the eight cysteines and catalytic histidines (H15 and H123) and lysine (K38) typically observed among members of the RNase A superfamily. Interesting trends include an unusually low number of synonymous substitutions (Ks) observed among the New World monkey RNase k6 genes. When considering nonsilent mutations, RNase k6 is a relatively stable lineage, with a nonsynonymous substitution rate of 0.40 × 10−9 nonsynonymous substitutions/nonsynonymous site/year (ns/ns/yr). These results stand in contrast to those determined for the primate orthologs of the two closely related ribonucleases, the eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), which have incorporated nonsilent mutations at very rapid rates (1.9 × 10−9and 2.0 × 10−9 ns/ns/yr, respectively). The uneventful trends observed for RNase k6 serve to spotlight the unique nature of EDN and ECP and the unusual evolutionary constraints to which these two ribonuclease genes must be responding.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF037081–AF037090.]
In Search of Human Variation
Authors: Weiss Kenneth M.
Published: May 2017

There is widespread interest in documenting the amount and geographic distribution of genetic variation in the human species. This information is desired by the biomedical community, who want a densely packed map of SNP (single nucleotidepolymorphism) sites to be used to identify genes associated with disease by linkage disequilibrium between sets of adjacent markers and the occurence of disease in populations, and to characterize disease-related variation among populations. Anthropologists use genetic variation to reconstruct our species’ history, and to understand the role of culture and geography in the global distribution of human variation. The requirements for these two perspectives seem to be converging on a need for an accessible, representative DNA bank and statistical database of human variation. However, both fields have been using conceptual models that are oversimplified, and this may lead to unrealistic expectations of the questions that can be answered from genetic data.
Mouse Palmitoyl Protein Thioesterase: Gene Structure and Expression of cDNA
Authors: Salonen Tarja , Hellsten Elina , Horelli-Kuitunen Nina , Peltonen Leena , Jalanko Anu
Published: May 2017

Palmitoyl protein thioesterase (PPT) is the defective enzyme in infantile neuronal ceroid lipofuscinosis (INCL), which is a recessively inherited, progressive neurodegenerative disorder. We present here the cloning, chromosomal mapping, genomic structure, and the expression of the cDNA of mouse PPT. The mouse PPT gene spans >21 kb of genomic DNA and contains nine exons with a coding sequence of 918 bp. Fluorescence in situ hybridization to metaphase chromosomes localized the mouse PPT gene to the chromosome 4 conserved syntenic region with human chromosome 1p32 where the human PPTis located. PPT is expressed widely in a variety of mouse tissues. The mouse PPT cDNA is conserved highly with the human and rat PPT both at the nucleotide and amino acid sequence level. Transient expression of mouse PPT in COS-1 cells yielded a 38/36-kD differentially glycosylated polypeptide that was also secreted into culture media. Immunofluorescence analysis of transiently transfected HeLa cells indicated lysosomal localization of mouse PPT. Based on the high conservation of the gene and polypeptide structure as well as similar processing and intracellular localization, the function of PPT in mouse and human are likely to be very similar.

[The sequence data described in this paper have been submitted to GenBank under accession no. AF071O25.]
Overlapping Genomic Sequences: A Treasure Trove of Single-Nucleotide Polymorphisms
Authors: Taillon-Miller Patricia , Gu Zhijie , Li Qun , Hillier LaDeana , Kwok Pui-Yan
Published: May 2017

An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21–7q22, and 13q12–13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AC003015 (for GS113423),AC002380 (GS330J10), AC000066 (RG293F11), AC003086 (RG104F04), AC002525(257C22A), and U73331 (96A18A).]
Analogous Enzymes: Independent Inventions in Enzyme Evolution
Authors: Galperin Michael Y. , Walker D. Roland , Koonin Eugene V.
Published: May 2017

It is known that the same reaction may be catalyzed by structurally unrelated enzymes. We performed a systematic search for such analogous (as opposed to homologous) enzymes by evaluating sequence conservation among enzymes with the same enzyme classification (EC) number using sensitive, iterative sequence database search methods. Enzymes without detectable sequence similarity to each other were found for 105 EC numbers (a total of 243 distinct proteins). In 34 cases, independent evolutionary origin of the suspected analogous enzymes was corroborated by showing that they possess different structural folds. Analogous enzymes were found in each class of enzymes, but their overall distribution on the map of biochemical pathways is patchy, suggesting multiple events of gene transfer and selective loss in evolution, rather than acquisition of entire pathways catalyzed by a set of unrelated enzymes. Recruitment of enzymes that catalyze a similar but distinct reaction seems to be a major scenario for the evolution of analogous enzymes, which should be taken into account for functional annotation of genomes. For many analogous enzymes, the bacterial form of the enzyme is different from the eukaryotic one; such enzymes may be promising targets for the development of new antibacterial drugs.
An Automated Hydrodynamic Process for Controlled, Unbiased DNA Shearing
Authors: Thorstenson Yvonne R. , Hunicke-Smith Scott P. , Oefner Peter J. , Davis Ronald W.
Published: May 2017

An automated, inexpensive, easy-to-use, and reproducible technique for controlled, random DNA fragmentation has been developed. The technique is based on point–sink hydrodynamics that result when a DNA sample is forced through a small hole by a syringe pump. Commercially available components are used to reduce the cost and complexity of the instrument. The design is optimized to reduce the volume of sample required and to speed processing time. Shearing of the samples can be completely automated by computer control. Ninety percent of sheared DNA fragments fall within a twofold size distribution that is highly reproducible. Three parameters are critical: the flow geometry, the flow rate, and a minimum number of iterations. Shearing is reproducible over a wide range of temperatures, DNA concentrations, and initial DNA size. The cloning efficiency of the sheared DNA is very good even without end repair, the distribution of assembled sequences is random, and there is no sequence bias at the ends of sheared fragments that have been cloned. The instrument, called thePoint–sink Shearer (PtS), has already been exported successfully to many other laboratories.
Comparative Gene Mapping: A Fine-Scale Survey of Chromosome Rearrangements between Ruminants and Humans
Authors: Schibler Laurent , Vaiman Daniel , Oustry Anne , Giraud-Delville Corinne , Cribiu Edmond P.
Published: May 2017

A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perform a genome-wide comparison between three mammalian orders. Twice as many rearrangements as revealed by ZOO-FISH were observed. The average size of conserved fragments could be estimated at 27 and 8 cm with humans and mice, respectively. The position of evolutionary breakpoints often correspond with human chromosome sites known to be vulnerable to rearrangement in neoplasia. Furthermore, 75 microsatellite markers, 30 of which were isolated from gene-containing bacterial artificial chromosomes (BACs), were added to the previous goat genetic map, achieving 88% genome coverage. Finally, 124 microsatellites were cytogenetically mapped, which made it possible to physically anchor and orient all the linkage groups. We believe that this comprehensive map will speed up positional cloning projects in domestic ruminants and clarify some aspects of mammalian chromosomal evolution.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. G40978–G41020,AF083170–AF083184, AF088286, AF08287, AF083401–AF083406, AF082884, and AF082885.]
Publication lag and early view effects in information science journals
Authors: Al Umut , Soydal Irem
Published: May 2017

Purpose

A major problem in today’s scholarly publishing process is the long tails for the assignment of volume and issue numbers for approved articles. The purpose of this paper is to investigate the extent to which information science journals offer early view features and the effects of these features.

Design/methodology/approach

The study addresses three basic questions: Do the articles approved for publication in information science journals appear in the online platforms of these journals before the assignment of volume and issue numbers? How long do the articles wait in the online platforms before they get the volume and issue numbers? Is there a statistically significant relationship between the online accessing numbers of the articles before they are published and bibliometric indicators?

Findings

More than half of the information science journals complete the editorial process in reasonable durations and share new articles with their readers before publishing them. In some journals, there are articles that wait for more than a year to be assigned volume and issue numbers after the completion of the editorial process. There are statistically significant differences, in terms of both their impact factor and immediacy index values, between the journals that offer early view features and those that do not. Both the impact factor and the immediacy index values of the journals that provide early view are higher than the others.

Practical implications

Adopting the early view policy may significantly help increase the impact factor and immediacy index values of the journals, as well as the visibility of their contents

Originality/value

The answers to this study’s research questions offer a new perspective to overcome the challenges in the processes through which scientific products meet with their users.
An extensive study of authorship authentication of Arabic articles
Authors: Al-Ayyoub Mahmoud , Alwajeeh Ahmed , Hmeidi Ismail
Published: May 2017

Purpose

The authorship authentication (AA) problem is concerned with correctly attributing a text document to its corresponding author. Historically, this problem has been the focus of various studies focusing on the intuitive idea that each author has a unique style that can be captured using stylometric features (SF). Another approach to this problem, known as the bag-of-words (BOW) approach, uses keywords occurrences/frequencies in each document to identify its author. Unlike the first one, this approach is more language-independent. This paper aims to study and compare both approaches focusing on the Arabic language which is still largely understudied despite its importance.

Design/methodology/approach

Being a supervised learning problem, the authors start by collecting a very large data set of Arabic documents to be used for training and testing purposes. For the SF approach, they compute hundreds of SF, whereas, for the BOW approach, the popular term frequency-inverse document frequency technique is used. Both approaches are compared under various settings.

Findings

The results show that the SF approach, which is much cheaper to train, can generate more accurate results under most settings.

Practical implications

Numerous advantages of efficiently solving the AA problem are obtained in different fields of academia as well as the industry including literature, security, forensics, electronic markets and trading, etc. Another practical implication of this work is the public release of its sources. Specifically, some of the SF can be very useful for other problems such as sentiment analysis.

Originality/value

This is the first study of its kind to compare the SF and BOW approaches for authorship analysis of Arabic articles. Moreover, many of the computed SF are novel, while other features are inspired by the literature. As SF are language-dependent and most existing papers focus on English, extra effort must be invested to adapt such features to Arabic text.
Your social network profile reveals you
Authors: Sander Tom , Teh Phoey Lee , Sloka Biruta
Published: May 2017

Purpose

This study aims to evaluate the fears of individuals on their profiles’ sharing in social network sites (SNSs), regarding its advantages and disadvantages. The researched issues are related with the employment seeking process. The concern of this study is the deviation observation between the fears acquired by the business and private social media members.

Design/methodology/approach

This study included an online survey with 236 respondents and calculated indicators of central tendency or location parameter, correlation coefficients and performed analysis of variance.

Findings

The result indicated and revealed the hidden danger and opportunities among social network members’ profile. This result addressed the need to consider the issue of user’s fears in reengineering the practical use of SNSs by organisations.

Research limitations/implications

Interesting for further research would be to transfer this research from the employment seeking process in other research fields to generalise the results more accurately.

Originality/value

The contribution to the research field is to compare different SNSs and to explain the reasons to use SNS profiles to support organisations by their decisions for a valuable strategy. This study provides an insight in use and behaviour of SNS members that support researchers to understand the behaviour of SNS members regarding their profile under consideration of the employment seeking process.
Organizational mimesis and the emergence of industry superannuation in Australia
Authors: Mees Bernard
Published: May 2017

Purpose

The purpose of this paper is to analyse the emergence of organizational isomorphism in the industry superannuation sector in Australia. The largest not-for-profit private businesses in the country, the industry funds were created in the 1980s in light of a broader union campaign to extend occupational retirement savings provision to all employees in Australia.

Design/methodology/approach

The emergence of organizational isomorphism among the industry funds is assessed from the perspective of institutional theory. The study is based on interviews with key players in the establishment of the industry superannuation sector, original archival research as well as contemporary public commentaries and more recent historical assessments.

Findings

The tripartite framework of institutional isomorphism established by DiMaggio and Powell is unable to explain the emergence of the widespread organizational isomorphism found in industry superannuation. Using the more recent notion of institutional logics allows a more satisfactory explanation for the convergence in models of retirement-savings provision in the industry superannuation sector.

Originality/value

Organizational isomorphism cannot be described simply in terms of a tripartite framework of professional normativity, state coercion and market-based mimesis. Alternatively governed organizations such as those created by trade unions may develop in a different manner than social enterprises founded by less powerful social actors.
Distressed Chinese firm prediction with discretized data
Authors: Huang Jun , Wang Haibo , Kochenberger Gary
Published: May 2017

Purpose

The authors develop a framework to build an early warning mechanism in detecting financial deterioration of Chinese companies. Many studies in the financial distress and bankruptcy prediction literature rarely do they examine the impact of pre-processing financial indicators on the prediction performance. The purpose of this paper is to address this shortcoming.

Design/methodology/approach

The proposed framework is evaluated by using both original and discretized data, and a least absolute shrinkage and selection operator (LASSO) selection technique for choosing an appropriate subset of financial ratios for improved predictive performance. The financial ratios are then analyzed by five different data mining techniques. Managerial insights, using data from Chinese companies, are revealed by the methodology employed.

Findings

The prediction accuracy increases after we discretized the continuous variables of financial ratios. A better prediction performance can be achieved by including fewer, but relatively more significant variables. Random forest has the highest overall performance following closely by SVM and neural network.

Originality/value

The contribution of this study is fourfold. First, the authors add to the literature on defaults by showing variable discretization to be an essential pre-processing step to improve the prediction performance for classification problems. Second, the authors demonstrate that machine learning approaches can achieve better performance than traditional statistical methods in classification tasks. Third, the authors provide the evidence for the adoption of C5.0 over other methods because rules generated with C5.0 provide managerial insights for managers. Finally, the authors demonstrate the effectiveness of the LASSO technique for identifying the most important financial ratios from each category, enabling one to build better predictive models.
The reference effect in newsvendor model with strategic customers
Authors: Liu Jiaming , Wu Chong , Su Tianyi
Published: May 2017

Purpose

The purpose of this paper is to discuss the role of reference effect on newsvendor’s decision behavior in a market with strategic customers and work out the newsvendor’s optimal pricing policy and ordering quantity.

Design/methodology/approach

This study utilizes the prospect theory and strategic customer framework to analyze the decision-making behavior on the newsvendor’s optimal pricing policy and ordering quantity. The paper further presents an extension of newsvendor model and provides the model’s properties. The paper finally analyzes the results with various parameters on the model and reports on the insights generated by the model.

Findings

The paper indicates that the ordering quantity is not altered with the changing proportion of strategic customers and myopic customers, but the ordering quantity and the pricing strategy are influenced in terms of newsvendor’s reference effect, loss aversion, product cost, and salvage price.

Practical implications

The research findings have important implications for decision makers. Previous researches have studied the incomplete rationality newsvendor’s decision-making behavior mainly by analyzing the vendor’s risk preferences or loss aversion, but the effect of reference point also plays an important role in analyzing the decision-maker’s behavior. The paper provides the optimal pricing policy and ordering quantity with the reference effect considering the strategic customers behavior. This model is also a valid complementarity to behavioral operations management research area.

Originality/value

The paper examines the role of reference effect in newsvendor problem with the strategic customers and analyzes the impact of parameters such as loss aversion on the newsvendor’s decision behavior.
Alliance success factors and performance in social economy enterprises
Authors: Bastida Ramon , Marimon Frederic , Tanganelli David
Published: May 2017

Purpose

Establishing alliances between social economy enterprises (SEEs) is considered to be a solution to the problem of providing enough resources and knowledge to compete in the global market and, at the same time, to maintain identity and ownership. Nevertheless, an important number of alliances breaks up after several years. Therefore, the purpose of this paper is to study the key factors that affect alliances’ development and outcome. In this study, the success factors that have been extensively tested in investor-owned companies are assessed in SEEs, which present important differences in organizational issues and corporate principles and values.

Design/methodology/approach

This study defines a scale that includes the most important factors that might be controlled by SEE managers to develop successful alliances. These factors are grouped into three categories: relational capital, relationship governance and the partner selection process. The study also assesses the impact of these factors on alliance performance.

Findings

Statistical analysis through structural equation modelling shows that relationship governance and the partner selection process have a significant impact on performance. Therefore, they can be considered success factors in alliances among SEEs.

Originality/value

Taking into account the relevant contribution of the SEEs to the European economy, and having noted the scarce number of studies about alliances success factors in the social economy sector, this study offers a significant contribution to this research field. Moreover, findings will be also interesting for SEE managers and social economy authorities when designing programmes to empower and support alliances.
Determinants of bank margins in a dual banking system
Authors: Lee Siew Peng , Isa Mansor
Published: May 2017

Purpose

The purpose of this paper is to determine of bank margins for conventional and Islamic banks in the dual banking system in Malaysia.

Design/methodology/approach

The study uses unbalanced panel data for 20 conventional banks and 16 Islamic banks over the period 2008-2014. The dynamic two-step GMM estimator technique introduced by Arellano and Bond (1991) is applied.

Findings

The results suggest that there are significant similarities with minor differences in terms of factors determining bank margins between conventional and Islamic banks in Malaysia. The margins for conventional banks are influenced by operating costs, efficiency, credit risk, degree of risk aversion, market share, size of operation, implicit interest payments and funding costs. For Islamic banks, the margin determinants are found to be operating costs, efficiency, credit risk, market share and implicit interest payments. This means that more factors influence the margins in conventional banks compared to Islamic banks. Although bank diversification activities have increased in recent years, their impact on bank margins is minimal.

Practical implications

The results suggest that improving operational costs, operational efficiency and credit risk management, and minimising implicit interest payments would be the best strategy to enhance the bank margins for both conventional and Islamic banks. The results also have important policy implications on the necessity to expand the size of Islamic banking in Malaysia.

Originality/value

There are relatively few studies concerning determinants of bank margins in emerging markets. The present study adds to the literature by presenting evidence from Malaysia, an emerging market with a dual banking system. This allows us to explore the similarities and differences between conventional and Islamic banks in Malaysia in respect of determinants of the margins.
Queering methodologies and organizational research: disrupting, critiquing, and exploring
Authors: McDonald James
Published: May 2017

Purpose

The purpose of this paper is to explore the methodological implications of queering organizational research. The author examines three related questions: what does queering organizational research entail?; how have organizational scholars queered research to date?; and how does queering organizational research and methodologies advance our understandings of organizing processes?

Design/methodology/approach

The paper begins with an overview of queer theory, which is followed by a review of the ways in which organizational research and methodologies have been and can be queered. The paper concludes with a discussion of the value of queering organizational research and methodologies and offers research questions that can guide future research that draws from queer theory.

Findings

The author claims that methodologies are queered through a researcher’s commitment to enacting the philosophical assumptions of queer theory in a research project. Much of the value of queering methodologies lies in its disruption and critique of conventional research practices, while enabling us to explore new ways of understanding organizational life.

Originality/value

Queer theory is still nascent but growing in organizational research. To date, there has been little consideration of the methodological implications of queering organizational research. This paper discusses these implications and can thus guide future research that is informed by queer theory.