bluuebunny/crossref_metadata_2025 huggingface dataset:
A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb
Authors: Bouffard Gerard G. , Idol Jacquelyn R. , Braden Valerie V. , Iyer Leslie M. , Cunningham Aimee F. , Weintraub Lauren A. , Touchman Jeffrey W. , Mohr-Tidwell Rose M. , Peluso Dale C. , Fulton Robert S. , Ueltzen Melinda S. , Weissenbach Jean , Magness Charles L. , Green Eric D.
Published: May 2017

The construction of highly integrated and annotated physical maps of human chromosomes represents a critical goal of the ongoing Human Genome Project. Our laboratory has focused on developing a physical map of human chromosome 7, a ∼170-Mb segment of DNA that corresponds to an estimated 5% of the human genome. Using a yeast artificial chromosome (YAC)-based sequence-tagged site (STS)-content mapping strategy, 2150 chromosome 7-specific STSs have been established and mapped to a collection of YACs highly enriched for chromosome 7 DNA. The STSs correspond to sequences generated from a variety of DNA sources, with particular emphasis placed on YAC insert ends, genetic markers, and genes. The YACs include a set of relatively nonchimeric clones from a human–hamster hybrid cell line as well as clones isolated from total genomic libraries. For map integration, we have localized 260 STSs corresponding to Genethon genetic markers and 259 STSs corresponding to markers ordered by radiation hybrid (RH) mapping on our YAC contigs. Analysis of the data with the program SEGMAP results in the assembly of 22 contigs that are “anchored” on the Genethon genetic map, the RH map, and/or the cytogenetic map. These 22 contigs are ordered relative to one another, are (in all but 3 cases) oriented relative to the centromere and telomeres, and contain >98% of the mapped STSs. The largest anchored YAC contig, accounting for most of 7p, contains 634 STSs and 1260 YACs. An additional 14 contigs, accounting for ∼1.5% of the mapped STSs, are assembled but remain unanchored on either the genetic or RH map. Therefore, these 14 “orphan” contigs are not ordered relative to other contigs. In our contig maps, adjacent STSs are connected by two or more YACs in >95% of cases. With 2150 mapped STSs, our map provides an average STS spacing of ∼79 kb. The physical map we report here exceeds the goal of 100-kb average STS spacing and should provide an excellent framework for systematic sequencing of the chromosome.

[Detailed information about the chromosome 7 physical map can be found at http://www.nhgri.nih.gov/DIR/GTB/CHR7or http://www.cshl.org/gr.]
An ∼1.2-Mb Bacterial Artificial Chromosome Contig Refines the Genetic and Physical Maps of the Lurcher Locus on Mouse Chromosome 6
Authors: De Jager Philip L. , Zuo Jian , Heintz Nathaniel
Published: May 2017

Lurcher (Lc) is a semidominant mouse mutant that displays a characteristic ataxia in the heterozygous state beginning in the third postnatal week. This symptom results from a neurodegenerative event in the cerebellum: There is a catastrophic loss of Purkinje cells in the heterozygote animal between postnatal days 10 and 15. In an effort to identify the genetic lesion borne by Lc mice, we initiated a cloning project based on the position of the Lcmutation on mouse chromosome 6. We have extended our previous analysis of the genomic segment containing the Lc locus by isolating a set of stable and manipulable genomic clones called bacterial artificial chromosomes (BACs) that cover this region of mouse chromosome 6. These clones provided a good substrate for the isolation of markers that were used to refine the physical map of the locus. Furthermore, 20 of these markers were mapped onto our (B6CBACa-Aw − J/A − Lc × CAST/Ei)F1 × B6CBACa-Aw − J/Abackcross, refining the genetic map and identifying two nonrecombinant markers (D6Rck354 and D6Rck355). These two markers, in conjunction with the closest flanking markers, were used to identify a 110-kb genomic segment that contains all four markers and hence contains the Lc locus. This small genomic segment, covered by multiple BACs, sets the stage for the final effort of this project—the identification of transcripts and of the mutation within theLc locus.

[The Lt1 sequence has been submitted to GenBank as two ESTs; the accession numbers are U89356 andU89357.]
A High-Resolution Physical and Transcript Map of the Cri du Chat Region of Human Chromosome 5p
Authors: Church Deanna M. , Yang Julie , Bocian Maureen , Shiang Rita , Wasmuth John J.
Published: May 2017

A high-resolution physical and transcription map has been generated of a 3.5-Mb region of 5p15.2 that is associated with the Cri du chat (CDC) syndrome. Utilizing a variety of resources including a natural deletion panel, a chromosome specific radiation hybrid panel, and YAC, PAC, and BAC genomic clones we have ordered >60 STSs within this region. Approximately 45% of these STSs were obtained from publicly available whole genome maps, thus allowing for integration of this map with currently available resources. Thirteen of these markers were ESTs. In addition, >70 exon trapped products have been mapped on the natural deletion panel and bacterial clone resource. The combination of these resources has allowed for the identification of 17 transcripts within this region, all of which represent candidate genes for CDC. Further characterization of the genomic contig also revealed that this region of 5p15 contains a large number of repetitive elements.

[The sequence data described in this paper have been submitted to GenBank under accession nos. G31374–G31412,B07604–B07657. On-line supplementary material concerning markers used, primers, PCR product sizes, and annealing conditions is available athttp://www.cshl.org/gr.]
Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome
Authors: Smith Douglas R. , Richterich Peter , Rubenfield Marc , Rice Philip W. , Butler Carol , Lee Hong-Mei , Kirst Susan , Gundersen Kristin , Abendschan Kari , Xu Qinxue , Chung Maria , Deloughery Craig , Aldredge Tyler , Maher James , Lundstrom Ronald , Tulig Craig , Falls Kathleen , Imrich Joan , Torrey Dana , Engelstein Marcy , Breton Gary , Madan Deepika , Nietupski Raymond , Seitz Bruce , Connelly Steven , McDougall Steven , Safer Hershel , Gibson Rene , Doucette-Stamm Lynn , Eiglmeier Karin , Bergh Staffan , Cole Stewart T. , Robison Keith , Richterich Laura , Johnson Jason , Church George M. , Mao Jen-i
Published: May 2017

The nucleotide sequence of 1.5 Mb of genomic DNA fromMycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to ∼66% completion. The sequences, derived from 43 recombinant cosmids, contain 1046 putative protein-coding genes, 44 repetitive regions, 3 rRNAs, and 15 tRNAs. The gene density of one per 1.4 kb is slightly lower than that ofMycoplasma (1.2 kb). Of the protein coding genes, 44% have significant matches to genes with well-defined functions. Comparison of 1157 M. leprae and 1564 Mycobacterium tuberculosisproteins shows a complex mosaic of homologous genomic blocks with up to 22 adjacent proteins in conserved map order. Matches to known enzymatic, antigenic, membrane, cell wall, cell division, multidrug resistance, and virulence proteins suggest therapeutic and vaccine targets. Unusual features of the M. leprae genome include large polyketide synthase (pks) operons, inteins, and highly fragmented pseudogenes.

[The sequence data described in this paper have been submitted to GenBank under accession nos. L78811–L78829,U00010–U00023, U15180–U15184, U15186, U15187, L01095, L01536, L04666, and L01263. On-line supplementary information for Table 1 is available at http://www.cshl.org/gr.]
Construction of P1-Derived Artificial Chromosome and Yeast Artificial Chromosome Contigs Encompassing the DFNB7 andDFNB11 Region of Chromosome 9q13–21
Authors: Greinwald John H. , Scott Daryl A. , Marietta Jacquie R. , Carmi Rivka , Manaligod Jose , Ramesh Arabandi , Zbar Ross I.S. , Kraft Michelle L. , Elbedour Khalil , Yairi Yael , Musy Maurice , Skvorak Anne B. , Van Camp Guy , Srisailapathy C.R. Srikumari , Lovett Michael , Morton Cynthia C. , Sheffield Val C. , Smith Richard J.H.
Published: May 2017

DFNB7 and DFNB11, two loci for autosomal recessive nonsyndromic hearing loss (ARNSHL), have been mapped to chromosome 9q13–21 in separate consanguineous families. Using a radiation hybrid map, we have determined the correct marker order in the DFNB7/11 region and have demonstrated that theDFNB11 locus resides within a redefined DFNB7interval. The gene(s) responsible for ARNSHL at these loci resides within an ∼1 cM interval bounded by markers D9S1806(centromeric) and D9S769 (telomeric). A recently discovered Indian family confirms the new telomeric boundary. To assist in the identification and cloning of candidate genes, YAC and PAC contigs were constructed. A total of 19 YAC and 23 PAC clones were utilized to span the affected region and ensure double coverage throughout. Twenty-two previously published STSs and 21 new STSs were used to determine marker order and confirm the integrity of the contig. Using a positional cloning strategy we have identified three cochlear expressed genes that map to the DFNB7/11 interval.
Development of a Comparative Genetic Linkage Map for Armigeres subalbatus Using Aedes aegyptiRFLP Markers
Authors: Ferdig Michael T. , Taft Andrew S. , Severson David W. , Christensen Bruce M.
Published: May 2017

One of the causative agents of lympahtic filariasis is the nematode parasite Brugia malayi that requires a competent mosquito vector for its development and transmission. Armigeres subalbatus mosquitoes rapidly destroy invading B. malayimicrofilariae via a defense response known as melanotic encapsulation. We have constructed a genetic linkage map for this mosquito species using RFLP markers from Aedes aegypti. This heterologous approach was possible because of the conserved nature of the coding sequences used as markers and provided an experimental framework to evaluate the hypothesis that linkage and gene order are conserved between these mosquito species. Of the 56 Ae. aegypti markers tested, 77% hybridize to genomic DNA digests of Ar. subalbatus under stringent conditions, with 53% of these demonstrating strain-specific polymorphisms. Twenty-six Ae. aegypti markers have been mapped using an F2- segregatingAr. subalbatus population derived from a cross of strains originating in Japan and Malaysia. Linear order of these marker loci is highly conserved between the two species. Only 1 of these markers, LF92, was not linked in the manner predicted by the Ae. aegypti map. In addition, the autosomal sex-determination locus that occurs in linkage group 1 in Ae. aegypti resides in group 3 in Ar. subalbatus. The Ar. subalbatus map provides a basic genetic context that can be utilized in further genetic studies to clarify the genetic basis of parasite resistance in this mosquito and is a necessary precursor to the identification of genome regions that carry genes that determine the encapsulation phenotype.

[The composite map and sequence database information for Ae. aegypti markers can be retrieved directly from the Ae. aegypti Genome Database through the World Wide Web: http://klab.agsci.colostate.edu.]
A Comparative Analysis of ABC Transporters in Complete Microbial Genomes
Authors: Tomii Kentaro , Kanehisa Minoru
Published: May 2017

The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an “ortholog group table” by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set for functional assignment in four additional genomes. In general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. InSynechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.
Mutation Detection by Ligation to Complete n-mer DNA Arrays
Authors: Gunderson Kevin L. , Huang Xiaohua C. , Morris Macdonald S. , Lipshutz Robert J. , Lockhart David J. , Chee Mark S.
Published: May 2017

A new approach to comparative nucleic acid sequence analysis is described that uses the ligation of DNA targets to high-density arrays containing complete sets of covalently attached oligonucleotides of length eight and nine. The combination of enzymatic or chemical ligation with a directed comparative analysis avoids many of the intrinsic difficulties associated with hybridization-based de novo sequence reconstruction methods described previously. Double-stranded DNA targets were fragmented and labeled to produce quasirandom populations of 5′ termini suitable for ligation and detection on the arrays. Kilobase-size DNA targets were used to demonstrate that complete n-mer arrays can correctly verify known sequences and can determine the presence of sequence differences relative to a reference. By use of 9-mer arrays, sequences of 1.2-kb targets were verified with >99.9% accuracy. Mutations in target sequences were detected by directly comparing the intensity pattern obtained for an unknown with that obtained for a known reference sequence. For targets of moderate length (1.2 kb), 100% of the mutations in the queried sequences were detected with 9-mer arrays. For higher complexity targets (2.5 and 16.6 kb), a relatively high percentage of mutations (90% and 66%, respectively) were correctly identified with a low false-positive rate of <0.03 percent. The methods described provide a general approach to analyzing nucleic acid samples on the basis of the interpretation of sequence-specific patterns of hybridization and ligation on complete n-mer oligonucleotide arrays.
Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3
Authors: Centola Michael , Chen Xiaoguang , Sood Raman , Deng Zuoming , Aksentijevich Ivona , Blake Trevor , Ricke Darrell O. , Chen Xiang , Wood Geryl , Zaks Nurit , Richards Neil , Krizman David , Mansfield Elizabeth , Apostolou Sinoula , Liu Jingmei , Shafran Neta , Vedula Anil , Hamon Melanie , Cercek Andrea , Kahan Tanaz , Gumucio Deborah , Callen David F. , Richards Robert I. , Moyzis Robert K. , Doggett Norman A. , Collins Francis S. , Liu P. Paul , Fischel-Ghodsian Nathan , Kastner Daniel L.
Published: May 2017

We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA aroundD16S3370, a marker showing a high degree of linkage disequilibrium with FMF, was sequenced to completion, and the sequence annotated. A transcript map reflecting the minimal number of genes encoded within the ∼700 kb of genomic DNA surrounding the FMF locus was assembled. This map consists of 27 genes with discreet messages detectable on Northerns, in addition to three olfactory-receptor genes, a cluster of 18 tRNA genes, and two putative transcriptional units that have typical intron–exon splice junctions yet do not detect messages on Northerns. Four of the transcripts are identical to genes described previously, seven have been independently identified by the French FMF Consortium, and the others are novel. Six related zinc-finger genes, a cluster of tRNAs, and three olfactory receptors account for the majority of transcribed sequences isolated from a 315-kb FMF central region (betweenD16S468/D16S3070and cosmid 377A12). Interspersed among them are several genes that may be important in inflammation. This transcript map not only has permitted the identification of the FMF gene (MEFV), but also has provided us an opportunity to probe the structural and functional features of this region of chromosome 16.
Mapping the Germ-Line and Somatic Genomes of a Ciliated Protozoan,Tetrahymena thermophila
Authors: Orias Eduardo
Published: May 2017

Ciliates are among the very few eukaryotes in which the powers of molecular biology, conventional genetics, and microbial methodology can be synergistically combined. Because ciliates also are distant relatives of vertebrates, fungi, and plants, the sequencing of a ciliate genome will be of import to our understanding of eukaryotic biology. Tetrahymena thermophila is the only ciliate in which a systematic genetic mapping of DNA polymorphisms has begun.Tetrahymena has many biological features that make it a specially or uniquely useful experimental system for fundamental research in cell and molecular biology and for biotechnological applications. A key factor in the usefulness of Tetrahymena is the speed, facility, and versatility with which it can be cultivated under a wide range of nutrient conditions, temperature, and scale. This article describes the progress made in genetically and physically mapping the genomes of T. thermophila: the micronuclear (germ-line) genome, which is not transcriptionally expressed, and the macronuclear (somatic) fragmented genome, which is actively expressed and determines the cell’s phenotype.
Genetic Studies in the Sleep Disorder Narcolepsy
Authors: Kadotani Hiroshi , Faraco Juliette , Mignot Emmanuel
Published: May 2017

Narcolepsy is a chronic neurologic disorder characterized by excessive daytime sleepiness and abnormal manifestations of REM sleep including cataplexy, sleep paralysis, and hypnagogic hallucinations. Narcolepsy is both a significant medical problem and a unique disease model for the study of sleep. Research in human narcolepsy has led to the identification of specific HLA alleles (DQB1*0602andDQA1*0102) that predispose to the disorder. This has suggested the possibility that narcolepsy may be an autoimmune disorder, a hypothesis that has not been confirmed to date. Genetic factors other than HLA are also likely to be involved. In a canine model of narcolepsy, the disorder is transmitted as a non-MHC single autosomal recessive trait with full penetrance (canarc-1). A tightly linked marker forcanarc-1has been identified, and positional cloning studies are under way to isolatecanarc-1from a newly developed canine genomic BAC library. The molecular cloning of this gene may lead to a better understanding of sleep mechanisms, as has been the case for circadian rhythms following the cloning offrq, per,andClock.
Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence
Authors: Kim Jin M. , Vanguri Swathi , Boeke Jef D. , Gabriel Abram , Voytas Daniel F.
Published: May 2017

We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs and the identification of a distinct Ty1 subfamily (Ty1′). Whereas Ty1, Ty2, and Ty5 LTRs displayed a broad range of sequence diversity (typically ranging from 70%–99% identity), Ty3 and Ty4 LTRs were highly similar within each element family (most sharing >96% nucleotide identity). Therefore, Ty3 and Ty4 may be more recent additions to the S. cerevisiae genome and perhaps entered through horizontal transfer or past polyploidization events. Distribution of Ty elements is distinctly nonrandom: 90% of Ty1, 82% of Ty2, 95% of Ty3, and 88% of Ty4 insertions were found within 750 bases of tRNA genes or other genes transcribed by RNA polymerase III. tRNA genes are the principle determinant of retrotransposon distribution, and there is, on average, 1.2 insertions per tRNA gene. Evidence for recombination was found near many Ty elements, particularly those not associated with tRNA gene targets. For these insertions, 5′- and 3′-flanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons can influence genome organization. S. cerevisiae offers the first opportunity to view organizational and evolutionary trends among retrotransposons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to other, more complex genomes.
Sequencing Multimegabase-Template DNA with BigDye Terminator Chemistry
Authors: Heiner Cheryl R. , Hunkapiller Kathryn L. , Chen Shiaw-Min , Glass John I. , Chen Ellson Y.
Published: May 2017

Using the recently introduced BigDye™ terminators, large-template DNA can be directly sequenced with custom primers on automated instruments. Cycle sequencing conditions are presented to sequence DNA samples isolated from a number of microbial genomes including 750-kb Ureaplasma urealyticum, 1.2-MbMycoplasma fermentans, 2.3-Mb Streptococcus pneumoniae, and 4.6-Mb Escherichia coli. Average read lengths of >700 bp from unique primer annealing sites are often sufficient to fill final gaps in microbial genome sequencing projects without additional manipulations of template DNA. The technique can also be applied to sequence-targeted regions, thereby bypassing tedious subcloning steps.
Short-Insert Libraries as a Method of Problem Solving in Genome Sequencing
Authors: McMurray Amanda A. , Sulston John E. , Quail Michael A.
Published: May 2017

As the Human Genome Project moves into its sequencing phase, a serious problem has arisen. The same problem has been increasingly vexing in the closing phase of the Caenorhabditis elegansproject. The difficulty lies in sequencing efficiently through certain regions in which the templates (DNA substrates for the sequencing process) form complex folded secondary structures that are inaccessible to the enzymes. The solution, however, is simply to break them up. Specifically, the offending fragments are sonicated heavily and recloned, as much smaller fragments, into pUC vector. The sequences obtained from the resulting library can subsequently be assembled, free from the effects of secondary structure, to produce high-quality, complete sequence. Because of the success and simplicity of this procedure, we have begun to use it for the sequencing of all regions in which standard primer walking has been at all difficult.

[The sequence data described in this paper have been submitted to the EMBL data library under accession nos. Z93392, Z92540, and Z81558.]
A Software System for Data Analysis in Automated DNA Sequencing
Authors: Giddings Michael C. , Severin Jessica , Westphall Michael , Wu Jiazhen , Smith Lloyd M.
Published: May 2017

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of ∼600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence.

[The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]
Genome Scan and Congenic Strains for Blood Pressure QTL Using Dahl Salt-Sensitive Rats
Authors: Garrett Michael R. , Dene Howard , Walder Roxanne , Zhang Qian-Yun , Cicila George T. , Assadnia Shahin , Deng Alan Y. , Rapp John P.
Published: May 2017

An F2 population (n = 151) derived from Dahl salt-sensitive (S) and Lewis rats was raised on a 8% NaCl diet for 9 weeks and analyzed for blood pressure quantitative trait loci (QTL) by use of a whole genome scan. Chromosomes 5 and 10 yielded lod scores for linkage to blood pressure that were significant; chromosomes 1, 2, 3, 8, 16, 17, and 18 gave lod scores suggestive for linkage. Chromosome 7 gave a significant signal for heart weight with a lesser effect on blood pressure. Congenic strains were constructed by introgressing Lewis low-blood-pressure QTL alleles for chromosomes 1, 5, 10, and 17 into the S genetic background. Congenic strains for chromosomes 1, 5, and 10 had significantly lower blood pressure than S, proving the existence of QTL on these chromosomes, but the chromosome 17 congenic strain failed to trap a contrasting QTL allele. The QTL allele increasing blood pressure originated from S rats for all QTL except those on chromosomes 2 and 7 in which the Lewis allele increased blood pressure. Interactions between each QTL and every other locus in the genome scan yielded significant interactions between chromosomes 10 and 4, and between chromosomes 2 and 3.
Parallel Radiation Hybrid Mapping: A Powerful Tool for High-Resolution Genomic Comparison
Authors: Yang Ya-Ping , Womack James E.
Published: May 2017

Comparative gene mapping in mammals typically involves identification of segments of conserved synteny in diverse genomes. The development of maps that permit comparison of gene order within conserved synteny has not advanced beyond the mouse map that takes advantage of linkage analysis in interspecific backcrosses. Radiation hybrid (RH) mapping provides a powerful tool for determining order of genes in genomes for which gene-based linkage mapping is impractical. Comparative RH mapping of 24 orthologous genes in this study revealed internal structural rearrangements between human chromosome 17 (HSA17) and bovine chromosome 19 (BTA19), two chromosomes known previously to be conserved completely and exclusively at level of synteny. Only six of the 24 genes had been previously ordered on the human G3 RH map. The use of the G3 panel to map the other 18, however, produced parallel RH maps for comparison of gene order at a resolution of <5 Mb on the bovine linkage map and from 1 to 3 Mb in the human physical map.
MerMade: An Oligodeoxyribonucleotide Synthesizer for High Throughput Oligonucleotide Production in Dual 96-Well Plates
Authors: Rayner Simon , Brignac Stafford , Bumeister Ron , Belosludtsev Yuri , Ward Travis , Grant O’dell , O’Brien Kevin , Evans Glen A. , Garner Harold R.
Published: May 2017

We have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. The machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. The run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nm. The reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. The two plates are placed in separate vacuum chucks and mounted on an xy table. Each well in turn is positioned under the appropriate reagent injection line and the reagent is injected by switching a dedicated valve. All aspects of machine operation are controlled by a Macintosh computer, which also guides the user through the startup and shutdown procedures, provides a continuous update on the status of the run, and facilitates a number of service procedures that need to be carried out periodically. Over 25,000 oligos have been synthesized for use in dye terminator sequencing reactions, polymerase chain reactions (PCRs), hybridization, and RT–PCR. Oligos up to 100 bases in length have been made with a coupling efficiency in excess of 99%. These machines, working in conjunction with our oligo prediction code are particularly well suited to application in automated high throughput genomic sequencing.
Microsatellite Marker Content Mapping of 12 Candidate Genes for Obesity: Assembly of Seven Obesity Screening Panels for Automated Genotyping
Authors: Winick Jeffrey D. , Friedman Jeffrey M.
Published: May 2017

Twin studies, adoption studies, and studies of familial aggregation indicate that obesity has a genetic component. Whereas, the genetic factors predisposing to obesity have been elucidated for several rare syndromes, the factors responsible for obesity in the general population have remained elusive. Genetic studies of complex traits are often accelerated by the use of candidate genes. To facilitate genetic studies of human obesity, seven multiplex panels of candidate genes for obesity that are suitable for fluorescent genotyping have been assembled. The multiplex panels are composed of 66 microsatellite markers linked tightly to 16 human gene products that are of potential importance in the control of body weight or linked to syndromic forms of obesity. As part of these efforts 12 previously cloned genes have been placed on the human physical map. In addition the chromosomal location of three of these genes, ART,NYP Y6R, and PPARγ, are reported for the first time. These resources will be of use in studies to identify the genetic factors responsible for human obesity. [Figures are available at http://www.genome.org.]
Exercising library and information literacies through alternate reality gaming
Authors: Jerrett Adam , Bothma Theo J.D. , de Beer Koos
Published: May 2017

Purpose

Teaching students/library patrons twenty-first century literacies (such as information and library literacies) is important within a library setting. As such, finding an appropriate manner to teach these skills in a practical manner at tertiary level is important. As vehicles for constructivist learning, games provide a unique opportunity to teach these twenty-first century literacies in an engaging, practical, format. The purpose of this paper is to discuss the implementation of an alternate reality game (ARG) to teach these literacies through gameplay.

Design/methodology/approach

An ARG was designed and developed where the core gameplay tasks taught and exercised twenty-first century literacies. The game, once completed, was then analysed as a case study to determine the effectiveness of the game-based approach to literacy learning.

Findings

Throughout the play of the game, players spent increasingly more time in the library, often using it as a common meeting point during play. Players reported that they learnt or exercised the skills that each game task focussed on, additionally noting that the game-based context made the process of learning and exercising these skills more enjoyable.

Originality/value

The findings suggest that the creation of games, whether real world or digital, may be useful in engaging students/patrons with twenty-first century literacies as well as with their local library. The documentation of a successful ARG to teach twenty-first century literacies provides a model for future research to follow when designing engaging library-oriented games.
Food logging: an information literacy perspective
Authors: Cox Andrew Martin , McKinney Pamela , Goodale Paula
Published: May 2017

Purpose

The purpose of this paper is to explore the meaning of information literacy (IL) in food logging, the activity of recording food intake and monitoring weight and other health conditions that may be affected by diet, using applications (apps) accessed through mobile devices and personal computers.

Design/methodology/approach

Data were gathered from a small group of food logging app users through a focus group and interviews. Analysis was informed by practice theory and the growing interest in IL outside educational settings.

Findings

Food logging revolves around the epistemic modality of information, but it is the user who creates information and it is not textual. Food logging is associated with a discourse of focussing on data and downplaying the corporeal information associated with eating and its effect on the body. Social information was an important source for choosing an app, but data were rarely shared with others. Food loggers are very concerned with data quality at the point of data entry. They have a strong sense of learning about healthy eating. They were not well informed about the data privacy and access issues.

Practical implications

Food loggers need to be better informed about data risks around food logging.

Originality/value

This is the first study of food logging from an IL perspective.
Design and evaluation of a movie recommendation system showing a review for evoking interested
Authors: Ishida Yuto , Uchiya Takahiro , Takumi Ichi
Published: May 2017

Purpose

In recent years, e-commerce (EC) sites dealing in various goods and services have increased along with internet popularity. Now, very few EC recommendation systems present a concrete reason for their recommendations. Therefore, because user preferences strongly influence outcomes, evaluation and selection are difficult for items, such as books, movies and luxury goods. The purpose of this paper is evoking interest by showing the review as a reason for a user’s decision-making factor. This paper aims to presents the development and introduction of a recommendation system that presents a review adapted to user preference.

Design/methodology/approach

The system presents a review to the user, which indicates the reason for matching the item contents and user preferences. Thereby, this system enables the creation of personalized reasons for recommendations.

Findings

Recommendation sentences conforming to user preferences are effective for item selection. Even with a simple method, in this paper, it was possible to present a review which is an item selection factor sufficient for the user.

Originality/value

This system can show a recommendation sentence that conforms to a user’s preferences merely from a user profile with the tag data of a product. This paper dealt in movies, but it can easily be applied even for other items.
ICT-FLAG: a web-based e-assessment platform featuring learning analytics and gamification
Authors: Gañán David , Caballé Santi , Clarisó Robert , Conesa Jordi , Bañeres David
Published: May 2017

Purpose

The purpose of this paper is to present an innovative web-based eLearning platform called ICT-FLAG that provides e-assessment tools with general-purpose formative assessment services featuring learning analytics and gamification.

Design/methodology/approach

The paper reports on the technical development of the platform driven by the Reference Model for Open Distributed Processing software methodology, which guides the platform construction, including the analysis and design steps.

Findings

The ICT-FLAG platform is technically tested by integrating it into a real e-assessment tool. Results are positive in terms of functional and non-functional aspects as well as user’s satisfaction on usability, emotional state, thus validating the platform as a valuable educational tool.

Research limitations/implications

Because of the chosen technical paper as article type, validation of the impact of the ICT-FLAG platform in the learning process is not provided. Ongoing research with this platform is to measure the learning outcomes of its use in a real context of eLearning.

Practical implications

The paper shows implications of the main technical issues and challenges encountered during the integration of the ICT-FLAG platform with external eLearning tools, involving relevant aspects of interoperability, security, modularity, scalability, portability and so on.

Originality/value

This platform can fill the gap of many e-assessment systems, which currently do not have built-in analytical and gamification tools for learning, thus providing them with the experience to improve the quality of education and learning.
Towards micro-foundations of institutional change
Authors: Bruce Kyle , von Staden Peter
Published: May 2017

Purpose

Given managerial choices and the sociocultural context in which they are made are at the heart of management history, then an understanding of both is critical. This paper argues that the “late” North (2005) provides such an understanding.

Design/methodology/approach

This study is a research review synthesizing much disparate but cognate literature across the new institutionalism in organizational sociology/studies and in economics.

Findings

“Late” North (2005) provides an important ontological frame for dealing with the so-called “paradox of embedded agency”, an approach that may afford management historians a more thorough account of how institutions are formed and change over time. North has always maintained that institutional change is the outcome of deliberate or intentional choices made by actors. However, and unlike his earlier work which ignores how humans come to make the said choices, North (2005) explicates the sociocognitive process by which intentionality emerges with expanded consciousness, as humans construct ideas and beliefs about reality, beliefs that shape decisions to alter the said reality via the process of institutional change.

Originality/value

It is rather curious that despite North’s status as a “historian”, management historians – or at least those publishing in this journal from its founding in 1995 – do not seem to be terribly interested in North’s work. Although North rates a mention in rival journals, other than Dagnino and Quattrone’s (2006) study, papers in this journal invoking institutional theory align with the new institutionalism in organizational sociology/studies (NIOS) rather than North’s new institutional economics (NIE). Even in the related sub-discipline of business history, those professing an interest in institutions are more interested in the NIE of non-historians Coase and Oliver Williamson than they are in North’s NIE. And, in recent work analysing the place and significance of institutional theory in historical research, the foundations are unmistakeably NIOS rather than North’s NIE.
Asset growth and the cross-section of stock returns: evidence from Greek listed firms
Authors: Constantinou Georgios , Karali Angeliki , Papanastasopoulos Georgios
Published: May 2017

Purpose

The purpose of this paper is to examine whether firm-level asset investment effects in returns found for US firms occur within the Greek stock market.

Design/methodology/approach

The paper utilizes portfolio-level tests and cross-sectional regressions.

Findings

The authors find that growth in total assets is strongly negatively related to future stock returns of Greek firms. In fact, the relation remains statistically significant, even when the authors control for other strong predictors of future returns (i.e. market capitalization and book-to-market ratio). Furthermore, the authors find that a hedge trading strategy on asset growth rate consisting of a long (short) position in firms with low (high) balance sheet growth generates positive returns, confirming that investment growth has significant predictive power for future returns of Greek listed firms.

Originality/value

The paper adds to the literature on the generalization of asset pricing regularities attributable to accounting figures in an emerging market.
SPACs: post-merger survival
Authors: Vulanovic Milos
Published: May 2017

Purpose

The purpose of this paper is to study how institutional characteristics of specified purpose acquisition companies (SPACs) are related to their post-merger survival. SPACs are unique financial firms that conduct the initial public offering (IPO) with the sole purpose of using the proceeds to acquire another private company. The paper finds that institutional characteristics of SPACs are important in determining post-merger outcomes of new company, specifically when it comes to their survival/failure, i.e., increases in pre-merger commitment by SPAC stakeholders and initial positive market performance increase post-merger survival likelihood; on the contrary, mergers with higher transaction costs and focused on foreign companies exhibit increased likelihood of failure.

Design/methodology/approach

Using unique sample of companies conducting an IPO, namely, SPACs, with the sole purpose to execute an acquisition in the future date within limited time, this paper presents additional evidence on the survival and acquisition frequency of IPOs, and determinants of these choices.

Findings

Observing unique set of specified purpose companies, this paper documents that SPACs’ failure rate is at the level of 58.09 percent, higher than any previously reported failure rate in the post-IPO survival literature and comparable only to failure rates found by Hensler et al. (1997) at 55.10 percent for general companies. In addition, the paper documents similar findings to Bhabra and Pettway (2003) that prospectus and market characteristics of original companies have predictive power with respect to survival.

Originality/value

This study extends the literature on post-IPO survival in following ways. First, the paper documents survival rates for unique set of companies organized with the sole purpose to acquire another company. Second, the paper presents evidence on how institutional characteristics of SPAC determine their post-merged outcomes, specifically when it comes to their failures. Finally, paper contributes to the scant literature on SPACs providing new evidence on their post-merger outcomes and performance.
Determinants of foreign-owned subsidiary performance in emerging economies
Authors: Dahms Sven
Published: May 2017

Purpose

The purpose of this study is to expand our understanding of performance determinants in foreign-owned subsidiaries (FOSs) located in an emerging economy.

Design/methodology/approach

A survey has been conducted of all known FOSs in Taiwan.

Findings

The results show that intra-organisational relationships and subsidiary competences are positively associated with various performance dimensions. Being located in a global city, as well as geographically distant from the home country, seem to have the opposite impact. The moderating factors of subsidiary age and authority are partially relevant.

Research limitations/implications

This study is based on a cross-sectional sample of FOSs in Taiwan.

Practical implications

The study shows that in an emerging market context, being strongly linked with the rest of the multinational enterprises might still be more conducive to subsidiary performance than venturing out. This is an important consideration, given the constant resource constraints for managers.

Practical implications

This study highlights important factors that ought to be taken into consideration by policymakers to attract suitable foreign direct investment.

Originality/value

This study provides a comprehensive test of major performance determinants for FOSs located in an emerging economy.
ANTi-History and the entrepreneurial work of privateers
Authors: Secord Peter , Corrigan Lawrence T.
Published: May 2017

Purpose

The purpose of this paper is to theorize the social role of management systems and their political connections using ANTi-History. In so doing, it engages with academic conversations around the writing of business history. The paper focuses on subjective experience in the context of colonial privateers and the vice-admiralty court in the Napoleonic Wars era.

Design/methodology/approach

ANTi-History is proposed as a theoretical lens to examine the entrepreneurial work of privateers. ANTi-History destabilizes the idea of history as a dominant account of the past and is interested in controversies as to how history is produced. This paper also brings-in Bourdieu’s notion of officialization because historical knowledge is situated in official practices that conceal translations and political strategies that enable actor-networks to act as one.

Findings

The controls of the vice-admiralty court not only perpetuated the inherited British class system, but also created versions of reality that came to be accepted as recorded history. This shows that the rules and regulations of the court were not neutral accounting activities. The systems constituted the identity of actors and produced privateer history as a modernist knowledge of the past and officialized by western, white, male, elites.

Originality/value

The “historic turn” in management and organization studies has not been fully realized more than a decade after its introduction. This paper engages with the historic turn by providing a specific exemplar of history as applied to officialized accounts of colonial privateers. Using ANTi-History as a methodological approach also makes a contribution by promoting it beyond a prolonged descriptive phase.
Typology of measures of children engagement in parental purchase decisions
Authors: Dikcius Vytautas , Pikturniene Indre , Reardon James
Published: May 2017

Purpose

Although there is a common agreement that children participate and impact parental purchase decisions, the research results are rather inconsistent. One of the reasons for the differences in the findings could be attributable to different operationalisations of a child engagement variable in surveys. This study aims to classify the instruments used to measure children engagement in parental purchase decisions and to develop a typology of these instruments.

Design/methodology/approach

In total, 67 articles that reported details and results of the surveys where a variable of children engagement in family decisions was operationalised were selected on a systematic basis. In total, 82 measures were extracted, reviewed and assigned to the particular category.

Findings

The typology of measures of children engagement into parental purchase decisions was developed. The features of particular measures, as well as their applicability for different types of child engagement measurement, are discussed.

Research limitations/implications

The sample of articles was limited to nine major scholarly databases and framed for 1985-2015, excluding conference presentations, dissertations, studies and other types of primary research publications.

Practical implications

The analysis demonstrates that authors who had seemingly similar or the same purpose of measuring variable of child engagement into parental purchase decision in fact have used different measures. The differences in measures tend to produce different size of engagement effect. The proposed typology will support scholarly community in establishing more clear definitions and measures of children engagement in parental purchase decision domain.

Originality/value

The typology of measures of children engagement into parental purchase decision is the first attempt to introduce systematised approach toward different domains within the field and their measurement.