bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple Members of a Third Subfamily of P-Type ATPases Identified by Genomic Sequences and ESTs
Authors: Halleck Margaret S. , Pradhan Deepti , Blackman Christie , Berkes Charlotte , Williamson Patrick , Schlegel Robert A.
Published: May 2017

The Saccharomyces cerevisiae genome contains five P-type ATPases divergent from both of the well-known subfamilies of these membrane ion transporters. This newly recognized third subfamily can be further divided into four classes of genes with nearly equal relatedness to each other. Genes of this new subfamily are also present and expressed in multicellular organisms such as Caenorhabditis elegans and mammals; some, but not all, can be assigned to the classes identified in yeast. Different classes of genes and different genes within a class are expressed differentially in tissues of the mouse. The recently cloned gene for the mammalian aminophospholipid translocase belongs to this new subfamily, suggesting that other subfamily members may transport other lipids or lipid-like molecules from one leaflet of the membrane bilayer to the other.
Analysis of EST-Driven Gene Annotation in Human Genomic Sequence
Authors: Bailey L. Charles , Searls David B. , Overton G. Christian
Published: May 2017

We have performed a systematic analysis of gene identification in genomic sequence by similarity search against expressed sequence tags (ESTs) to assess the suitability of this method for automated annotation of the human genome. A BLAST-based strategy was constructed to examine the potential of this approach, and was applied to test sets containing all human genomic sequences longer than 5 kb in public databases, plus 300 kb of exhaustively characterized benchmark sequence. At high stringency, 70%–90% of all annotated genes are detected by near-identity to EST sequence; >95% of ESTs aligning with well-annotated sequences overlap a gene. These ESTs provide immediate access to the corresponding cDNA clones for follow-up laboratory verification and subsequent biologic analysis. At lower stringency, up to 97% of annotated genes were identified by similarity to ESTs. The apparent false-positive rate rose to 55% of ESTs among all sequences and 20% among benchmark sequences at the lowest stringency, indicating that many genes in public database entries are unannotated. Approximately half of the alignments span multiple exons, and thus aid in the construction of gene predictions and elucidation of alternative splicing. In addition, ESTs from multiple cDNA libraries frequently cluster over genes, providing a starting point for crude expression profiles. Clone IDs may be used to form EST pairs, and particularly to extend models by associating alignments of lower stringency with high-quality alignments. These results demonstrate that EST similarity search is a practical general-purpose annotation technique that complements pattern recognition methods as a tool for gene characterization.
Xenoduplex Analysis—A Method for Comparative Gene Mapping Using Hybrid Panels
Authors: Marklund Lena , Jeon Jin-Tae , Andersson Leif
Published: May 2017

Somatic cell hybrid (SCH) panels and radiation hybrid (RH) panels are powerful resources for comparative gene mapping because gene assignments are made without the detection of genetic polymorphism as needed for linkage mapping. A frequently encountered problem, however, is that the gene specific primers may amplify homologous PCR products of equal length from the donor and recipient species of the panel. Here, we describe a simple solution to this problem in which we utilize the formation of interspecies heteroduplexes that can be easily distinguished from the corresponding homoduplexes by native polyacrylamide gel electrophoresis. We denote these DNA–DNA interspecies hybrids, xenoduplexes (xeno = Gr. Xenos, foreigner). A merit of the method is that the formation of xenoduplexes strongly suggests that the PCR products from the two species represent homologous sequences. The method is thus particularly useful for comparative gene mapping when the PCR primers have been designed by use of sequence information from other species. In this study we have successfully used xenoduplex analysis and a pig-rodent SCH panel to map seven porcine genes (ACADM, AT3, HOXD, IL8RB, LEPR, PAX8, PKLR) for which no previous sequence information was available. The assignment of the leptin receptor gene (LEPR) to pig chromosome 6q32–35 excluded LEPR as a candidate gene for a QTL on pig chromosome 4 with a major effect on fatness.
Dispersed Repetitive DNA Has Spread to New Genomes Since Polyploid Formation in Cotton
Authors: Zhao Xin-ping , Si Yang , Hanson Robert E. , Crane Charles F. , Price H. James , Stelly David M. , Wendel Jonathan F. , Paterson Andrew H.
Published: May 2017

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AF060571–AF060667 and U31112–U31113.]
A Map of 75 Human Ribosomal Protein Genes
Authors: Kenmochi Naoya , Kawaguchi Tomoko , Rozen Steve , Davis Elizabeth , Goodman Nathan , Hudson Thomas J. , Tanaka Tatsuo , Page David C.
Published: May 2017

We mapped 75 genes that collectively encode >90% of the proteins found in human ribosomes. Because localization of ribosomal protein genes (rp genes) is complicated by the existence of processed pseudogenes, multiple strategies were devised to identify PCR-detectable sequence-tagged sites (STSs) at introns. In some cases we exploited specific, pre-existing information about the intron/exon structure of a given human rp gene or its homolog in another vertebrate. When such information was unavailable, selection of PCR primer pairs was guided by general insights gleaned from analysis of all mammalian rp genes whose intron/exon structures have been published. For many genes, PCR amplification of introns was facilitated by use of YAC pool DNAs rather than total human genomic DNA as templates. We then assigned the rp gene STSs to individual human chromosomes by typing human–rodent hybrid cell lines. The genes were placed more precisely on the physical map of the human genome by typing of radiation hybrids or screening YAC libraries. Fifty-one previously unmapped rp genes were localized, and 24 previously reported rp gene localizations were confirmed, refined, or corrected. Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes. Chromosome 19, known to have a high gene density, contains an unusually large number of rp genes (12). This map provides a foundation for the study of the possible roles of ribosomal protein deficiencies in chromosomal and Mendelian disorders.

[The sequence data described in this paper have been submitted to GenBank. They are listed in Table 1.]
A Homogeneous, Ligase-Mediated DNA Diagnostic Test
Authors: Chen Xiangning , Livak Kenneth J. , Kwok Pui-Yan
Published: May 2017

Single-nucleotide variations are the most widely distributed genetic markers in the human genome. A subset of these variations, the substitution mutations, are responsible for most genetic disorders. As single nucleotide polymorphism (SNP) markers are being developed for molecular diagnosis of genetic disorders and large-scale population studies for genetic analysis of complex traits, a simple, sensitive, and specific test for single nucleotide changes is highly desirable. In this report we describe the development of a homogeneous DNA detection method that requires no further manipulations after the initial reaction is set up. This assay, named dye-labeled oligonucleotide ligation (DOL), combines the PCR and the oligonucleotide ligation reaction in a two-stage thermal cycling sequence with fluorescence resonance energy transfer (FRET) detection monitored in real time. Because FRET occurs only when the donor and acceptor dyes are in close proximity, one can infer the genotype or mutational status of a DNA sample by monitoring the specific ligation of dye-labeled oligonucleotide probes. We have successfully applied the DOL assay to genotype 10 SNPs or mutations. By designing the PCR primers and ligation probes in a consistent manner, multiple assays can be done under the same thermal cycling conditions. The standardized design and execution of the DOL assay means that it can be automated for high-throughput genotyping in large-scale population studies.
Emerging Patterns of Comparative Genome Organization in Some Mammalian Species as Revealed by Zoo-FISH
Authors: Chowdhary Bhanu P. , Raudsepp Terje , Frönicke Lutz , Scherthan Harry
Published: May 2017

Although gene maps for a variety of evolutionarily diverged mammalian species have expanded rapidly during the past few years, until recently it has been difficult to precisely define chromosomal segments that are homologous between species. A solution to this problem has come from the development of Zoo-FISH, also known as cross-species chromosome painting. The use of Zoo-FISH to identify regions of chromosomal homology has allowed the transfer of information from map-rich species such as human and mouse to a wide variety of other species. From a Zoo-FISH analysis spanning four mammalian orders (Primates, Artiodactyla, Carnivora, and Perissodactyla), and involving eight species (human, pig, cattle, Indian muntjac, cat, American mink, harbor seal, and horse), three distinct classes of synteny conservation have been designated: (1) conservation of whole chromosome synteny, (2) conservation of large chromosomal blocks, and (3) conservation of neighboring segment combinations. This analysis has also made it possible to identify a set of chromosome segments (based on human chromosome equivalents) that probably made up the karyotype of the common ancestor of the four orders. This approach provides a basis for developing a picture of the ancestral mammalian karyotype, but a full understanding will depend on studies encompassing more diverse combinations of mammalian orders.
Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes
Authors: Mushegian Arcady R. , Garey James R. , Martin Jason , Liu Leo X.
Published: May 2017

Comparisons of DNA and protein sequences between humans and model organisms, including the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit flyDrosophila melanogaster, are a significant source of information about the function of human genes and proteins in both normal and disease states. Important questions regarding cross-species sequence comparison remain unanswered, including (1) the fraction of the metabolic, signaling, and regulatory pathways that is shared by humans and the various model organisms; and (2) the validity of functional inferences based on sequence homology. We addressed these questions by analyzing the available fractions of human, fly, nematode, and yeast genomes for orthologous protein-coding genes, applying strict criteria to distinguish between candidate orthologous and paralogous proteins. Forty-two quartets of proteins could be identified as candidate orthologs. Twenty-four Drosophila protein sequences were more similar to their human orthologs than the corresponding nematode proteins. Analysis of sequence substitutions and evolutionary distances in this data set revealed that most C. elegans genes are evolving more rapidly than Drosophila genes, suggesting that unequal evolutionary rates may contribute to the differences in similarity to human protein sequences. The available fraction ofDrosophila proteins appears to lack representatives of many protein families and domains, reflecting the relative paucity of genomic data from this species.
Evidence for the Presence of Insulin-Dependent Diabetes-Associated Alleles on the Distal Part of Mouse Chromosome 6
Authors: Melanitou Evie , Joly Florence , Lathrop Mark , Boitard Christian , Avner Philip
Published: May 2017

Type 1 diabetes (IDDM) is a complex disorder with multifactorial and polygenic etiology. A genome-wide screen performed in a BC1 cohort of a cross between the nonobese diabetic (NOD) mouse with the diabetes-resistant feral strain PWK detected a major locus contributing to diabetes development on the distal part of chromosome 6. Unlike the majority of otherIddloci identified in intraspecific crosses, susceptibility is associated with the presence of the PWK allele. Genetic linkage analysis of congenic lines segregating PWK chromosome 6 segments in a NOD background confirmed the presence of theIddlocus within this region. The genetic interval defined by analysis of congenic animals showed a peak of significant linkage (P = 0.0005) centered on an ∼9-cM region lying between D6Mit11 and D6Mit25 genetic markers within distal mouse chromosome 6.

[Genetic markers polymorphic between the NOD and PWK strains are available as a supplement athttp://www.genome.org]
Vector–Hexamer PCR Isolation of All Insert Ends from a YAC Contig of the MouseIgh Locus
Authors: Herring Christopher D. , Chevillard Christophe , Johnston Sean L. , Wettstein Peter J. , Riblet Roy
Published: May 2017

We have developed a simple PCR strategy, termed vector–hexamer PCR, that is unique in its ability to easily recover every insert end from large insert clones in YAC and BAC vectors. We used this method to amplify and isolate all insert ends from a YAC contig covering the mouseIghlocus. Seventy-seven ends were amplified and sequenced from 36 YAC clones from four libraries in the pYAC4 vector. Unexpectedly, 40% of the insert ends of these YACs were LINE1 repeats. Nonrepetitive ends were suitable for use as probes on Southern blots of digested YACs to identify overlaps and construct a contig. The same strategy was used successfully to amplify insert ends from YACs in the pRML vector from the Whitehead Institute/MIT-820 mouse YAC library and from BACs in pBeloBAC11. The simplicity of this technique and its ability to isolate every end from large insert clones are of great utility in genomic investigation.

[The nucleotide sequence data reported in this paper are accessible in GenBank under accession nos.B07512–B07598.]
Functional Genomics in the Mouse: Phenotype-Based Mutagenesis Screens
Authors: Schimenti John , Bucan Maja
Published: May 2017

Significant progress has been made in sequencing the genomes of several model organisms, and efforts are now underway to complete the sequencing of the human genome. In parallel with this effort, new approaches are being developed for the elucidation of the functional content of the human genome. The mouse will have an important role in this phase of the genome project as a model system. In this review we discuss and compare classical genetic approaches to gene function—phenotype-based mutagenesis screens aimed at the establishment of a large collection of single gene mutations affecting a wide range of phenotypic traits in the mouse. Whereas large scale genome-wide screens that are directed at the identification of all loci contributing to a specific phenotype may be impractical, region-specific saturation screens that provide mutations within a delimited chromosomal region are a feasible alternative. Region-specific screens in the mouse can be performed in only two generations by combining high-efficiency chemical mutagenesis with deletion complexes generated using embryonic stem (ES) cells. The ability to create and analyze deletion complexes rapidly, as well as to map novel chemically-induced mutations within these complexes, will facilitate systematic functional analysis of the mouse genome and corresponding gene sequences in humans. Furthermore, as the extent of the mouse genome sequencing effort is still uncertain, we underscore a necessity to direct sequencing efforts to those chromosomal regions that are targets for extensive mutagenesis screens.
Radiation Hybrid Mapping of the Two Highly Homologous Human–Variant pMCHL Genes by PCR–SSCP
Authors: Miller Christine L. , Thompson Robert C. , Burmeister Margit
Published: May 2017

When gene loci are very similar in sequence, as in gene families or multiple pseudogenes, it is difficult to determine the specific location of the individual genes. We show here that applying PCR–SSCP to a radiation hybrid panel allowed mapping and specific sequencing of two genes with only a few sequence differences. Human–variant forms of the promelanin-concentrating hormone (pMCH) gene are found in two locations in the genome, previously localized by FISH to 5p14 and 5q12–q13. Without prior knowledge of sequence variation between the loci, we observed a difference in migration pattern in PCR–SSCP, indicating the presence of at least one point of sequence divergence. PCR–SSCP of 93 samples from a human–hamster radiation hybrid panel revealed the location of the genes to be between markers WI-4804 and AFM225YC5 on chromosome 5p, and between markers WI-3133 and WI-4225 on chromosome 5q. Sequencing of the two 680-bp PCR products from the hybrid panel demonstrated 3 bases of sequence difference between the 5p and 5q locations.

[The data described in this paper for thepMCHL2 gene have been submitted to the GenBank data library under accession no. AF064698.]
Complete Sequence of a 93.4-kb Contig from Chromosome 3 of Trypanosoma cruzi Containing a Strand-Switch Region
Authors: Andersson Björn , Åslund Lena , Tammi Martti , Tran Anh-Nhi , Hoheisel Jörg D. , Pettersson Ulf
Published: May 2017

We have initiated large-scale sequencing of the third smallest chromosome of the CL Brener strain of Trypanosoma cruzi and we report here the complete sequence of a contig consisting of three cosmids. This contig covers 93.4 kb and has been found to contain 20–30 novel genes and several repeat elements, including a novel chromosome 3-specific 400-bp repeat sequence. The intergenic sequences were found to be rich in di- and trinucleotide repeats of varying lengths and also contained several known T. cruzi repeat elements. The sequence contains 29 open reading frames (ORFs) longer than 700 bp, the longest being 5157 bp, and a large number of shorter ORFs. Of the long ORFs, seven show homology to known genes in parasites and other organisms, whereas four ORFs were confirmed by sequencing of cDNA clones. Two shorter ORFs were confirmed by a database homology and a cDNA clone, respectively, and one RNA gene was identified. The identified genes include two copies of the gene for alanine-aminotransferase as well as genes for glucose-6-phosphate isomerase, protein kinases and phosphatases, and an ATP synthase subunit. An interesting feature of the sequence was that the genes appear to be organized in two long clusters containing multiple genes on the same strand. The two clusters are transcribed in opposite directions and they are separated by an ∼20-kb long, relatively GC-rich sequence, that contains two large repetitive elements as well as a pseudogene for cruzipain and a gene for U2snRNA. It is likely that this strand switch region contains one or more regulatory and promoter regions. The reported sequence provides the first insight into the genome organization of T. cruzi and shows the potential of this approach for rapid identification of novel genes.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF052831–AF052833.]
A Comprehensive, High-Resolution Genomic Transcript Map of Human Skeletal Muscle
Authors: Bortoluzzi Stefania , Rampoldi Luca , Simionati Barbara , Zimbello Rosanna , Barbon Alessandro , d’Alessi Fabio , Tiso Natascia , Pallavicini Alberto , Toppo Stefano , Cannata Nicola , Valle Giorgio , Lanfranchi Gerolamo , Danieli Gian Antonio
Published: May 2017

We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data retrieved from UniGene with the RH mapping information on 46 novel muscle transcripts, which showed no similarity to any known sequence. In the map, distances are expressed in megabase pairs. About one-quarter of the map entries represents putative novel genes. Genes known to be specifically expressed in muscle account for <4% of the total. The genomic distribution of the map entries confirmed the previous finding that muscle genes are selectively concentrated in chromosomes 17, 19, and X. Five chromosomal regions are suspected to have a significant excess of muscle genes. Present data support the hypothesis that the biochemical and functional properties of differentiated muscle cells may result from the transcription of a very limited number of muscle-specific genes along with the activity of a large number of genes, shared with other tissues, but showing different levels of expression in muscle.

[The sequence data described in this paper have been submitted to the EMBL data library under accession nos. F23198–F23242.]
The Synuclein Family
Authors: Lavedan Christian
Published: May 2017

The synuclein gene family recently came into the spotlight, when one of its members, α-synuclein, was found to be mutated in several families with autosomal dominant Parkinson’s disease (PD). A peptide of the α-synuclein protein had been characterized previously as a major component of amyloid plaques in brains of patients with Alzheimer’s disease (AD). The mechanism by which this presynaptic protein is involved in the two most common neurodegenerative disorders, AD and PD, remains unclear. Remarkably, another member of this gene family, γ-synuclein, has been shown to be overexpressed in breast carcinomas and may also be overexpressed in ovarian cancer. The possible involvement of the synuclein proteins in the etiology of common human diseases has raised exciting questions and is the subject of intense investigation. Details of the properties of any member of the synuclein family may provide useful information for understanding the characteristics and function of other family members. The present review offers a synopsis of the current state of knowledge of all synuclein family members in different species.
Imprinting Mechanisms
Authors: Constância Miguel , Pickard Benjamin , Kelsey Gavin , Reik Wolf
Published: May 2017

A number of recent studies have provided new insights into mechanisms that regulate genomic imprinting in the mammalian genome. Regions of allele-specific differential methylation (DMRs) are present in all imprinted genes examined. Differential methylation is erased in germ cells at an early stage of their development, and germ-line-specific methylation imprints in DMRs are reestablished around the time of birth. After fertilization, differential methylation is retained in core DMRs despite genome-wide demethylation and de novo methylation during preimplantation and early postimplantation stages. Direct repeats near CG-rich DMRs may be involved in the establishment and maintenance of allele-specific methylation patterns. Imprinted genes tend to be clustered; one important component of clustering is enhancer competition, whereby promoters of linked imprinted genes compete for access to enhancers. Regional organization and spreading of the epigenotype during development is also important and depends on DMRs and imprinting centers. The mechanism of cis spreading of DNA methylation is not known, but precedent is provided by theXist RNA, which results in X chromosome inactivation incis. Reading of the somatic imprints could be carried out by transcription factors that are sensitive to methylation, or by methyl–cytosine-binding proteins that are involved in transcriptional repression through chromatin remodeling.
Compositional Heterogeneity within, and Uniformity between, DNA Sequences of Yeast Chromosomes
Authors: Li Wentian , Stolovitzky Gustavo , Bernaola-Galván Pedro , Oliver José L.
Published: May 2017

The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by the size distribution of domains, coding density, size distribution of open reading frames, spatial power spectra, and deviation from binomial distribution for C + G% in large moving windows that there is a strong deviation of the yeast sequences from random sequences. For the latter, not only do we graphically illustrate the similarity for the above mentioned statistics, but we also carry out a rigorous analysis of variance (ANOVA) test. The hypothesis that all yeast chromosomes are similar cannot be rejected by this test. We examine the two possible explanations of this interchromosomal uniformity: a common origin, such as genome-wide duplication (polyploidization), and a concerted evolutionary process.
Duplication of a Genomic Region Containing the Cdc2L1-2 and MMP21-22 Genes on Human Chromosome 1p36.3 and their Linkage to D1Z2
Authors: Gururajan Rajagopal , Lahti Jill M. , Grenet Jose , Easton John , Gruber Irmhild , Ambros Peter F. , Kidd Vincent J.
Published: May 2017

Cdc2L1 and Cdc2L2 span ∼140 kb on human chromosome 1p36.3. The products of the Cdc2L genes encode almost identical protein kinases, the PITSLRE kinases, which have functions that may be relevant to the regulation of transcription/splicing and apoptotic signaling. These genes are deleted/translocated in neuroblastomas with MYCN gene amplification, a subset of malignant melanomas, and in a newly delineated deletion syndrome. Here we report that the p36.3 region of human chromosome 1 consists of two identical genomic regions, each of which contain a Cdc2L gene linked to ametalloprotease (MMP) gene in a tail-to-tail configuration. This duplicated genomic region is also linked tightly to D1Z2, a genetic marker containing a highly polymorphic VNTR (variable number tandemrepeat) consisting of an unusual 40-bp reiterated sequence. Thus, these genes and the polymorphic marker D1Z2 are organized as follows: telomere–D1Z2–5′-MMP22-3′–3′-Cdc2L2-5′–5′-Cdc2L1-3′– 3′-MMP21-5′–centromere. Remarkably, the introns and exons of Cdc2L1 and Cdc2L2, as well as their flanking regions, are essentially identical. A total of 15 amino acid differences, 12 nonconservative and 3 conservative, can be found in the 773–786 amino acids specified by the various products of theCdc2L genes. Two separate promoter/5′ untranslated (UT) regions, CpG1 and CpG2, are identical to a reported previously methylated genomic CpG sequence and are used to express >20 different Cdc2L transcripts from the two genes. The expression of CpG2 transcripts from Cdc2L1 and Cdc2L2 is tissue/cell-line specific. CpG1 transcripts are expressed ubiquitously from both genes, with perhaps some bias towards the expression of CpG1Cdc2L1 mRNAs in certain hematopoietic cells.

[The sequence data described in this paper have been submitted to the GenBank data library under the following accession nos.: (cDNAs)AF067511–AF067529; (genomic) AF080678–AF080697.]
Physical and Comparative Mapping of Distal Mouse Chromosome 16
Authors: Cabin Deborah E. , McKee-Johnson Jennifer W. , Matesic Lydia E. , Wiltshire Tim , Rue Elizabeth E. , Mjaatvedt Anne E. , Huo Yong Kang , Korenberg Julie R. , Reeves Roger H.
Published: May 2017

Distal mouse Chromosome 16 (Chr. 16) includes a region of conserved linkage with human Chromosome 21 (Chr. 21). Mouse models of Down syndrome based on trisomy of distal Chr. 16 have several phenotypes similar to those seen in human patients and have proven useful for correlating dosage imbalance of specific genes with specific developmental anomalies. The degree to which such findings can be related to Down syndrome depends on how well the conserved synteny is maintained. Twenty-four genes have been mapped in both species and there are no discordancies, but the region could carry hundreds of genes. Comparative sequence represents the ultimate comparative map and will aid in identification of genes and their regulatory sequences. A physical map of the distal 4.5 Mb of Chr. 16 has been assembled as an essential step toward a map of sequence-ready templates. The map consists of 51 YACs and 15 BACs and includes 18 transcripts, 9 of which are mapped for the first time in mouse, and 3 of which are, for the first time, described in either species. YAC fragmentation was used to precisely localize the 49 markers on the map. Comparison of this physical map with that of the corresponding region on Chr. 21 shows conservation not only of gene order but of size in the 3 Mb fromCbr1 to Ets2; distal to Ets2, the human map is expanded.

[The sequence data described in this paper have been submitted to GenBank. See Tables 1 and 2 for accession nos.]
A Primary Male Autosomal Linkage Map of the Horse Genome
Authors: Lindgren Gabriella , Sandberg Kaj , Persson Helena , Marklund Stefan , Breen Matthew , Sandgren Björn , Carlstén Johan , Ellegren Hans
Published: May 2017

A primary male autosomal linkage map of the domestic horse (Equus caballus) has been developed by segregation analysis of 140 genetic markers within eight half-sib families. The family material comprised four Standardbred trotters and four Icelandic horses, with a total of 263 offspring. The marker set included 121 microsatellite markers, eight protein polymorphisms, five RFLPs, three blood group polymorphisms, two PCR–RFLPs, and one single strand conformation polymorphism (SSCP). One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different chromosomes (ECA1, ECA2, ECA3, ECA4, ECA5, ECA6, ECA7, ECA9, ECA10, ECA11, ECA13, ECA15, ECA16, ECA18, ECA19, ECA21, ECA22, and ECA30). The average distance between linked markers was 12.6 cM and the longest linkage group measured 103 cM. The total map distance contained within linkage groups was 679 cM. If the distances covered outside the ends of linkage groups and by unlinked markers were included, it was estimated that the marker set covered at least 1500 cM, that is, at least 50% of the genome. A comparison of the relationship between genetic and physical distances in anchored linkage groups gave ratios of 0.5–0.8 cM per Mb of DNA. This would suggest that the total male recombinational distance in the horse is 2000 cM; this value is lower than that suggested by chiasma counts. The present map should provide an important framework for future genome mapping in the horse.
Information systems security practices in social software applications
Authors: Tamrin Suraya Ika , Norman Azah Anir , Hamid Suraya
Published: May 2017

Purpose

The purpose of this paper to investigate the current information systems security (ISS) practices of the social software application (SSA) users via the internet.

Design/methodology/approach

The paper opted for a systematic literature review survey on ISS and its practices in SSAs between 2010 and 2015. The study includes a set of 39 papers from among 1,990 retrieved papers published in 35 high-impact journals. The selected papers were filtered using the Publish or Perish software by Harzing and Journal Citation Report (JCR) with an inclusion criterion of least one citation per article.

Findings

The practice of ISS is driven by the need to protect the confidentiality, integrity, and availability of the data from being tampered. It is coherent with the current practice as reported by many researchers in this study. Four important factors lead to the ISS practice in SSA: protection tools offered, ownership, user behaviour, and security policy.

Practical implications

The paper highlights the implication of successful ISS practices is having clear security purpose and security supported environment (user behaviour and security protection tools) and governance (security policy and ownership) protection tools offered, ownership, user behaviour, and security policy towards ISS practice by the users.

Originality/value

This paper fulfils an identified need to study how to enable ISS practice.
Evaluation of an IoT-based e-learning testbed
Authors: Yamada Masafumi , Cuka Miralda , Liu Yi , Oda Tetsuya , Matsuo Keita , Barolli Leonard
Published: May 2017

Purpose

This paper aims to present the design and implementation of an Internet of Things (IoT)-based e-learning testbed using Raspberry Pi mounted on Raspbian operating system (OS).

Design/methodology/approach

The testbed is composed of five Raspberry Pi B+ computers. The experiments are carried out in the department floor considering an non line of sight (NLoS) environment. Single constant bit rate (CBR) flows were transmitted over user datagram protocol (UDP), and data were collected for five metrics: throughput, packet delivery ratio (PDR), hop count, delay and jitter using the Iperf.

Findings

The implemented testbed was evaluated using experiments. The experimental results showed that the nodes in the testbed were communicating smoothly, and by using attention value, the learner concentration is increased.

Research limitations/implications

The performance of the Optimized Link State Routing (OLSR) protocol was analyzed in a floor environment considering the NLoS scenario. However, this testbed can be implemented to other protocols also.

Originality/value

Because of the opportunities provided by the internet, people are taking advantage of e-learning courses, and enormous research efforts have been dedicated to the development of e-learning systems. To date, many e-learning systems are proposed and used practically. However, in these systems, the e-learning completion rate is low. To deal with this problem, an IoT-based e-learning system was implemented to increase the e-learning completion ratio by increasing the learner concentration.
Transitioning business school accounting from binary divide to unified national system
Authors: Safari Maryam , Parker Lee David
Published: May 2017

Purpose

This paper aims to provide a historical case study of strategic changes in accounting at an Australian university’s business school department during 1972-1992 when it was repositioning itself in the early stages of major changes in the Australian and international tertiary accounting education environment. The study is conducted within the context of the university history within which the department operated as well as major government policy and global education shifts shaping university structures and focus.

Design/methodology/approach

This study offers a historical analysis of early stage changes in university focus at the business school’s accounting department, developed through departmental and university reports and oral history interviews. A narrative analytical methodology is adopted to portray a history of an academic accounting department in transition.

Findings

This case study illuminates the impacts of and responses to the beginning of marketisation and globalisation of higher education, and the commercialisation of universities and explains the strategic implementation processes in one university’s business school departmental during a period of significant formative change in the Australian accounting education landscape.

Originality/value

This study deepens our understanding of environmental, structural, educational and research changes at the operational departmental level of academic institutions, paying particular attention to the organisational culture and human capital dimensions.
An exploration into the relationship between management and market forces
Authors: Bowden Bradley
Published: May 2017

Purpose

Are business outcomes due primarily to entrepreneurial and managerial ability or are they mainly the result of business content? The purpose of this study is to explore this question by comparing the railroads of Victoria and Queensland (Australia) and the South-West and Northern Plains of America between 1881 and 1900. Given the commonalities of the four railway systems in terms of their economic orientation towards rural custom, and their marked difference in terms of ownership, one would expect similarities in their financial circumstances if outcomes were primarily determined by fluctuations in global commodity markets. Conversely, marked differences would be expected if outcomes primarily resulted from managerial initiative.

Design/methodology/approach

Conceptually, this study is informed by the idea that social and economic outcomes are shaped by long historical movements, with meaningful structural change occurring rarely but to great effect. In exploring this concept through a comparison of the railways of Australia and the American West, the study draws on two forms of archival evidence. One source of evidence relates to railroad management, operations and finances. Figures cited come primarily from Australian railway commissioners’ reports and Poor’s Manual of the Railroads of the USA. The other source of evidence relates to agricultural statistics. These are drawn from official reports.

Findings

This study argues that effective strategic decision-making can only occur if we understand the structural changes that alter our world. In the late nineteenth century, the Australian and American railroads servicing newly settled rural regions were financial failures because management failed to appreciate the structural changes that the revolution in steam-powered transport had initiated; a revolution which resulted in commodity prices – and hence, the railway rates for farm produce – being determined by global demand and supply balances rather than by local factors. As a result, they continued a policy of expansion that was no longer financially justified.

Originality/value

This study seeks to contribute to a fundamental debate in historical studies and management about the drivers of social and economic change. Increasingly, there is acceptance of the view that historical circumstances are inherently unstable and what counts is the particular change cascading through a myriad of “events”. This study points in a contrary direction, suggesting that business outcomes are primarily determined by deep structural shifts that can be understood and steered but seldom opposed.
Where do high-impact ideas come from? The interplay between the cumulative knowledge structures and search strategies of researchers
Authors: Wang Le , Lin Jun , Yan Jie , Cui Wentian
Published: May 2017

Purpose

The purpose of this paper is to investigate the combined effects of different modalities of long-term knowledge accumulation and short-term knowledge searching on the generation of high-impact ideas. The authors aim at providing useful conclusions for academic scholars.

Design/methodology/approach

Two dimensions of the cumulative knowledge structures of researchers are measured: knowledge depth and knowledge breadth. The search strategies employed by researchers are classified as local search and distant search. The authors use researchers’ historical publications to measure cumulative knowledge structures. References contained in these publications serve as an indicator of knowledge searching behaviors and are used to measure search strategies. Highly cited papers with random-but-matched papers from the same journal published in the same year are adopted to test the hypotheses.

Findings

The knowledge depth of researchers positively predicts the generation of high-impact ideas. Knowledge breadth has a bell-shaped relationship to the generation of high-impact ideas. Two instances of “strategic fit” between the knowledge structures and search strategies of researchers are identified; namely, knowledge breadth combines most effectively with local search, and knowledge depth combines most effectively with distant search in generating high-impact ideas.

Research limitations/implications

Using article references to measure authors’ knowledge search behaviors may lead to biases. Future research should perform a survey to obtain a comprehensive understanding of the knowledge search behaviors of scholars.

Practical implications

A “T-shaped” knowledge structure in the long run is recommended for maximal generation of high-impact ideas. Researchers who have not adopted this optimal knowledge structure can employ a matched search strategy to leverage their existing knowledge structures.

Originality/value

This paper is among the first to examine the interactive effects between the cumulative knowledge structures and short-term knowledge searching strategies of researchers. The authors have enriched the exploration and exploitation theory by adding the dimension of time into the analysis.
An improved fuzzy decision analysis framework with fuzzy Mahalanobis distances for individual investment effect appraisal
Authors: Chen Shang-Yu
Published: May 2017

Purpose

Due to such issues as the recent economic recession, low salaries, and an aging society, how people can strengthen their investment performance when managing their personal financial affairs is a critical consideration. The purpose of this paper is to consider the assessment of the performance of individual investment policies and to present an evaluation framework for measuring the degree of workability of investment policies.

Design/methodology/approach

The proposed evaluation framework combines the fuzzy analytical hierarchy process and the improved fuzzy technique for order preference by similarity to the ideal solution to measure the efficiency scores of the alternatives (i.e. investment policies) under assessment.

Findings

This quantitative framework is formed from the criteria of investment return, taxation, risk, and individual circumstances according to prudent evaluation of private wealth management research, and is applied to appraise the investment performance of individuals in Taiwan. The findings indicate that investment performance, risks, and the investment of mutual funds are the most preferred conditions and investment policy for investors, and can offer some effective suggestions for investors as well as for future academic research.

Originality/value

The efficiency scores are computed based on the fuzzy Mahalanobis distances, taking into account the fuzzy correlations among experts’ criteria. The advantage of adopting the fuzzy Mahalanobis distances over the fuzzy Euclidean distances, which are typically computed in the literature, is that the undulation of the efficiency scores can be reduced.
The influence of organizational factors on board roles
Authors: Sánchez Leticia Pérez-Calero , Guerrero-Villegas Jaime , Hurtado González José Manuel
Published: May 2017

Purpose

Using a contingency approach, the purpose of this paper is to study how organizational factors (such as the organizational life cycle, firm size, firm ownership concentration and firm technology) determine the relative importance of the monitoring and provision of resources roles provided by board members.

Design/methodology/approach

This paper highlights the importance of contingency factors in carrying out board’s roles using a sample of 579 European firms registered in the STOXX Europe 600 index. The authors used a longitudinal analysis for the period from 2002 through to 2011.

Findings

The results show that the monitoring role is more relevant for companies that are large, are operating at the mature and stagnant stages, have a dispersed ownership and are low-technology. However, the provision of resources role is more relevant for companies that are in the growth and stagnant stages, and have a concentrated ownership.

Originality/value

The traditional analysis that relates the board’s structure and composition to the board’s roles focuses on determining what board should be the best. It plays little attention to analyzing which organizational factors affect the importance and presence of monitoring or resource dependence roles. In this regard, this work adds significant insights to agency theory and resource dependence theory as, with a contingency framework, the research aims to find what functions the board needs to develop in order to get better firm performance.
Uncorporates: changes in master limited partnerships
Authors: Kendall Lynn K. , Rogers Nina
Published: May 2017

Purpose

The purpose of this paper is to examine how major changes in an industry may differentially affect firms based on their organizational structure. The authors examine midstream oil and gas firms, comparing master limited partnerships (MLPs or uncorporates) with more traditional midstream corporate firms when the industry changed from one that was considered mature to a more rapid growth industry.

Design/methodology/approach

Non-parametric comparisons of returns, distributions, and operating ratios are presented across the two organizational forms and across two distinct industry activity periods. The risk-adjusted return analysis, including Fama and French factors, incorporates a wild bootstrap to address heteroscedasticity in the data.

Findings

In the industry’s mature market period, partnerships provided a significantly greater payout, return, return on equity (ROE), cash flow, and lower leverage, while exhibiting lower levels of systematic risk than corporations. In the later growth period, midstream corporations and partnerships are no longer significantly different in their returns, ROE or margins. MLPs now have significantly higher leverage levels, while continuing to provide significantly higher dividend payouts.

Originality/value

The paper contributes to the literature with an analysis of the effects of a changing industry environment on two different organizational types across a common industry. The authors find that the optimal organizational structure may be dependent on the environment. The findings during the initial period are consistent with prior research comparing publicly traded partnerships and corporations. During the growth phase, the findings lend support to the seminal literature with respect to corporations potentially best-suited to “growth” industries, while highlighting specific results by organizational form.