cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104447.v1
title: Supplementary Material for: In silico Analysis of 2085 Clones from a Normalized Rat Vestibular Periphery 3′ cDNA Library

description: The inserts from 2400 cDNA clones isolated from a normalized <i>Rattus norvegicus</i> vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3′ cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa’s ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5′ end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function.
DOI: 10.6084/m9.figshare.5104456.v1
title: Supplementary Material for: Intracranial Navigation Using a Novel Device for Endoscope Fixation and Targeting: Technical Innovation

description: Intracranial endoscopy involves point-to-point navigation: first, in the introduction of the endoscope into a cerebrospinal fluid-containing space and, second, in the identification of a target structure. We report testing and preliminary clinical use of a device for the direct cranial fixation and point-to-point neuronavigation of a rigid ventricular endoscope. An 18-month-old female child presented with rapidly progressive macrocephaly, developmental delay and left hemiparesis. Neuroimaging revealed a large suprasellar cyst and obstructive hydrocephalus. We adapted a ball-stem device with an endoscopic working channel for direct cranial fixation over a burr hole. This device was successfully used in conjunction with MR-based neuronavigation to fenestrate the cyst. Seven months after the operation her developmental delay, macrocephaly and hemiparesis resolved. This device may be particularly effective in cases of small ventricles, ambiguous intra-ventricular landmarks, and in children too young for head-holder immobilization.
DOI: 10.6084/m9.figshare.5104435
title: Supplementary Material for: Molecular evolution of the human chromosome 15 pericentromeric region

description: We present a detailed molecular evolutionary analysis of 1.2 Mb from the pericentromeric region of human 15q11. Sequence analysis indicates the region has been subject to extensive interchromosomal and intrachromosomal duplications during primate evolution. Comparative FISH analyses among non-human primates show remarkable quantitative and qualitative differences in the organization and duplication history of this region – including lineage-specific deletions and duplication expansions. Phylogenetic and comparative analyses reveal that the region is composed of at least 24 distinct segmental duplications or duplicons that have populated the pericentromeric regions of the human genome over the last 40 million years of human evolution. The value of combining both cytogenetic and experimental data in understanding the complex forces which have shaped these regions is discussed.
DOI: 10.6084/m9.figshare.5104444.v1
title: Supplementary Material for: The structures of mouse and human L1 elements reflect their insertion mechanism

description: L1 is an abundant, interspersed repeated DNA element of mammalian genomes. It has achieved its high copy number via retrotransposition. Like other non-LTR retrotransposons, L1 insertion into chromosomal DNA apparently occurs by target-site primed reverse transcription, or TPRT. L1 retrotransposition often generates elements with 5′ truncations that are flanked by a duplication of the genomic target site (TSD). It is typically assumed that the 5′ truncated elements are the consequence of poor processivity of the L1 reverse transcriptase. However, we find that the majority of young L1 elements from both the human and mouse genomes are truncated at sequences that can basepair with the target site. Thus, to whatever extent truncation is a consequence of poor processivity, we suggest that truncation is likely to occur when target site sequence can basepair with L1 sequence. This finding supports a model for insertion that occurs by two sequential TPRT reactions, the second of which relies upon the homology between the target site and L1. Because perfect heteroduplex formation is not required for all insertions, a dynamic relationship between the primer, template and enzyme during reverse transcription is inferred. 5′ truncation may be a successful evolutionary strategy that is exploited by L1 as a means to escape host suppression of transposition.
DOI: 10.6084/m9.figshare.5104453.v1
title: The probability of the wing damage in the dragonfly Sympetrum vulgatum (Anisoptera: Libellulidae): a field study (Suppl data)

description: This file contains the wings investigated in our "The probability of the wing damage in the dragonfly Sympetrum vulgatum (Anisoptera: Libellulidae): a field" study. Please, do not hesitate to contact me at harajabi@hotmail.com, if you have any question.
DOI: 10.6084/m9.figshare.5104423
title: Supplementary Material for: The Complete Genome Sequence of <i> Bacillus licheniformis </i>DSM13, an Organism with Great Industrial Potential

description: The genome of <i>Bacillus licheniformis </i>DSM13 consists of a single chromosome that has a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were identified. The genome shows a marked co-linearity with <i>Bacillus subtilis </i>but contains defined inserted regions that can be identified at the sequence as well as at the functional level. <i>B. licheniformis </i>DSM13 has a well-conserved secretory system, no polyketide biosynthesis, but is able to form the lipopeptide lichenysin. From the further analysis of the genome sequence, we identified conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the presence of anaerobic ribonucleotide reductase explaining that <i>B. licheniformis </i>is able to grow on acetate and 2,3-butanediol as well as anaerobically on glucose. Many new genes of potential interest for biotechnological applications were found in <i>B. licheniformis</i>; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes.
DOI: 10.6084/m9.figshare.5104429
title: Supplementary Material for: Evolutionary implications of pericentromeric gene expression in humans

description: Human pericentromeric sequences are enriched for recent sequence duplications. The continual creation and shuffling of these duplications can create novel intron-exon structures and it has been suggested that these regions have a function as gene nurseries. However, these sequences are also rich in satellite repeats which can repress transcription, and analyses of chromosomes 10 and 21 have suggested that they are transcript poor. Here, we investigate the relationship between pericentromeric duplication and transcription by analyzing the in silico transcriptional profiles within the proximal 1.5 Mb of genomic sequence on all human chromosome arms in relation to duplication status. We identify an ∼5× excess of transcripts specific to cancer and/or testis in pericentromeric duplications compared to surrounding single copy sequence, with the expression of &gt;50% of all transcripts in duplications being restricted to these tissues. We also identify an ∼5× excess of transcripts in duplications which contain large quantities of interspersed repeats. These results indicate that the transcriptional profiles of duplicated and single copy sequences within pericentromeric DNA are distinct, suggesting that pericentromeric instability is unlikely to represent a common route for gene creation but may have a disproportionate effect upon genes whose function is restricted to the germ line.
DOI: 10.6084/m9.figshare.5104432
title: Supplementary Material for: Identity by descent and DNA sequence variation of human SINE and LINE elements

description: To test the hypothesis that Alu and L1 elements are genetic characters that are essentially homoplasy-free, we sequenced a total of five human L1 elements and eleven recently integrated Alu elements from 160 chromosomes (80 individuals representing four diverse human populations). Analysis of worldwide samples at L1 loci revealed 292 segregating sites and a nucleotide diversity of 0.0050. For Ya5 Alu loci, there were 129 segregating sites and nucleotide diversity was estimated at 0.0045. The Alu and L1 sequence diversity varied element to element. No completely or partially deleted Alu or L1 alleles were identified during the analysis. These data suggest that mobile element insertions are identical by descent characters for the study of human population genetics.
DOI: 10.6084/m9.figshare.5104426
title: Supplementary Material for: Microglia in Culture: What Genes Do They Express?

description: The cell culture model utilized in this study represents one of the most widely used paradigms of microglia in vitro. After 14 days, microglia harvested from the neonatal rat brain are considered ‘mature’. However, it is clear that this represents a somewhat arbitrary definition. In this paper, we provide a transcriptome definition of such microglial cells. More than 7,000 known genes and 1,000 expressed sequence tag clusters were analysed. ‘Microglia genes’ were defined as sequences consistently expressed in all microglia samples tested. Accordingly, 388 genes were identified as microglia genes. Another 1,440 sequences were detected in a subset of the cultures. Genes consistently expressed by microglia included genes known to be involved in the cellular immune response, brain tissue surveillance, microglial migration as well as proliferation. The expression profile reported here provides a baseline against which changes of microglia in vitro can be examined. Importantly, expression profiling of normal microglia will help to provide the presently purely operational definition of ‘microglial activation’ with a molecular biological correlate. Furthermore, the data reported here add to our understanding of microglia biology and allow projections as to what functions microglia may exert in vivo, as well as in vitro.
DOI: 10.6084/m9.figshare.5104429.v1
title: Supplementary Material for: Evolutionary implications of pericentromeric gene expression in humans

description: Human pericentromeric sequences are enriched for recent sequence duplications. The continual creation and shuffling of these duplications can create novel intron-exon structures and it has been suggested that these regions have a function as gene nurseries. However, these sequences are also rich in satellite repeats which can repress transcription, and analyses of chromosomes 10 and 21 have suggested that they are transcript poor. Here, we investigate the relationship between pericentromeric duplication and transcription by analyzing the in silico transcriptional profiles within the proximal 1.5 Mb of genomic sequence on all human chromosome arms in relation to duplication status. We identify an ∼5× excess of transcripts specific to cancer and/or testis in pericentromeric duplications compared to surrounding single copy sequence, with the expression of &gt;50% of all transcripts in duplications being restricted to these tissues. We also identify an ∼5× excess of transcripts in duplications which contain large quantities of interspersed repeats. These results indicate that the transcriptional profiles of duplicated and single copy sequences within pericentromeric DNA are distinct, suggesting that pericentromeric instability is unlikely to represent a common route for gene creation but may have a disproportionate effect upon genes whose function is restricted to the germ line.
DOI: 10.6084/m9.figshare.5104432.v1
title: Supplementary Material for: Identity by descent and DNA sequence variation of human SINE and LINE elements

description: To test the hypothesis that Alu and L1 elements are genetic characters that are essentially homoplasy-free, we sequenced a total of five human L1 elements and eleven recently integrated Alu elements from 160 chromosomes (80 individuals representing four diverse human populations). Analysis of worldwide samples at L1 loci revealed 292 segregating sites and a nucleotide diversity of 0.0050. For Ya5 Alu loci, there were 129 segregating sites and nucleotide diversity was estimated at 0.0045. The Alu and L1 sequence diversity varied element to element. No completely or partially deleted Alu or L1 alleles were identified during the analysis. These data suggest that mobile element insertions are identical by descent characters for the study of human population genetics.
DOI: 10.6084/m9.figshare.5104435.v1
title: Supplementary Material for: Molecular evolution of the human chromosome 15 pericentromeric region

description: We present a detailed molecular evolutionary analysis of 1.2 Mb from the pericentromeric region of human 15q11. Sequence analysis indicates the region has been subject to extensive interchromosomal and intrachromosomal duplications during primate evolution. Comparative FISH analyses among non-human primates show remarkable quantitative and qualitative differences in the organization and duplication history of this region – including lineage-specific deletions and duplication expansions. Phylogenetic and comparative analyses reveal that the region is composed of at least 24 distinct segmental duplications or duplicons that have populated the pericentromeric regions of the human genome over the last 40 million years of human evolution. The value of combining both cytogenetic and experimental data in understanding the complex forces which have shaped these regions is discussed.
DOI: 10.6084/m9.figshare.5104420
title: Supplementary Material for: Identifying differentially expressed genes in the mammalian retina and the retinal pigment epithelium by suppression subtractive hybridization

description: Retina and retinal pigment epithelium (RPE) cells are of neuroectodermal origin with highly specialized functions in light perception. Identification and characterization of genes differentially expressed in these cells will greatly aid our understanding of their functional roles in retinal biology. As a source enriched for gene transcripts from the retina/RPE, we generated a human retina and a bovine RPE cDNA library applying the PCR-based technique of suppression subtractive hybridization (SSH). Sequencing of 1,080 retina and 2,350 RPE SSH clones resulted in the identification of 321 and 343 non-redundant human transcripts, respectively. Of these, only 27 genes were in common between the two cDNA libraries. One transcript expressed exclusively in retina and RPE is the novel gene C4orf11 which is comprised of four exons on chromosome 4q21.2. We report the full-length cloning of two isoforms of C4orf11, 919 bp and 857 bp in length, both of which contain four identical open reading frames (ORFs). While ORFs 1 to 3 show no homologies to known proteins or protein domains, ORF4 reveals 50% sequence identity to RPE-spondin, a hypothetical protein on 8q13.3 with unknown function. We demonstrate that both the retina and the RPE SSH cDNA libraries are excellent resources for identifying known and novel genes exclusively or abundantly expressed in the retina/RPE complex. In combination with other approaches such as microarray analysis or serial analysis of gene expression (SAGE), the availability of highly sensitive and specific SSH cDNA libraries will facilitate the comprehensive description of the retina/RPE transcriptome.
DOI: 10.6084/m9.figshare.5104423.v1
title: Supplementary Material for: The Complete Genome Sequence of <i> Bacillus licheniformis </i>DSM13, an Organism with Great Industrial Potential

description: The genome of <i>Bacillus licheniformis </i>DSM13 consists of a single chromosome that has a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were identified. The genome shows a marked co-linearity with <i>Bacillus subtilis </i>but contains defined inserted regions that can be identified at the sequence as well as at the functional level. <i>B. licheniformis </i>DSM13 has a well-conserved secretory system, no polyketide biosynthesis, but is able to form the lipopeptide lichenysin. From the further analysis of the genome sequence, we identified conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the presence of anaerobic ribonucleotide reductase explaining that <i>B. licheniformis </i>is able to grow on acetate and 2,3-butanediol as well as anaerobically on glucose. Many new genes of potential interest for biotechnological applications were found in <i>B. licheniformis</i>; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes.
DOI: 10.6084/m9.figshare.5104411
title: Supplementary Material for: ICAM-3 Activation Modulates Cell-Cell Contacts of Human Bone Marrow Endothelial Cells

description: The Ig-like cell adhesion molecule ICAM-3 is mainly expressed on human leukocytes and is involved in cell-cell interactions. Its expression on endothelium is observed during disorders such as Crohn’s disease and in solid tumors. We found low but detectable expression of ICAM-3 on VE-cadherin-expressing cells from primary human bone marrow aspirates, i.e. endothelial cells, and on primary human endothelial cells from cord blood. Also, immortalized human umbilical cord endothelial cells and human bone marrow endothelial cells showed ICAM-3 expression. However, its function on human endothelium is not known. Surprisingly, activation of endothelial ICAM-3 by crosslinking with specific antibodies resulted in a drop in the electrical resistance of bone marrow endothelial monolayers. In line with this, immunocytochemical analysis showed a loss of endothelial cell-cell contacts after ICAM-3 crosslinking in HBMEC. Detailed biochemical analysis showed an association of moesin and in a later stage ezrin with ICAM-3 upon crosslinking in HBMEC. Moreover, ICAM-3 crosslinking induced the production of reactive oxygen species (ROS), which are known to be involved in the control of endothelial cell-cell contacts. In conclusion, we showed that ICAM-3 is expressed on human bone marrow endothelial cells and controls endothelial integrity via ROS-dependent signaling.
DOI: 10.6084/m9.figshare.5104417
title: Supplementary Material for: Systems biology of the 2-cell mouse embryo

description: The transcriptome of the 2-cell mouse embryo was analyzed to provide insight into the molecular networks at play during nuclear reprogramming and embryonic genome activation. Analysis of ESTs from a 2-cell cDNA library identified nearly 4,000 genes, over half of which have not been previously studied. Transcripts of mobile elements, especially those of LTR retrotransposons, are abundantly represented in 2-cell embryos, suggesting their possible role in introducing genomic variation, and epigenetic restructuring of the embryonic genome. Analysis of Gene Ontology of the 2-cell-stage expressed genes outlines the major biological processes that guide the oocyte-to-embryo transition. These results provide a foundation for understanding molecular control at the onset of mammalian development.
DOI: 10.6084/m9.figshare.5104426.v1
title: Supplementary Material for: Microglia in Culture: What Genes Do They Express?

description: The cell culture model utilized in this study represents one of the most widely used paradigms of microglia in vitro. After 14 days, microglia harvested from the neonatal rat brain are considered ‘mature’. However, it is clear that this represents a somewhat arbitrary definition. In this paper, we provide a transcriptome definition of such microglial cells. More than 7,000 known genes and 1,000 expressed sequence tag clusters were analysed. ‘Microglia genes’ were defined as sequences consistently expressed in all microglia samples tested. Accordingly, 388 genes were identified as microglia genes. Another 1,440 sequences were detected in a subset of the cultures. Genes consistently expressed by microglia included genes known to be involved in the cellular immune response, brain tissue surveillance, microglial migration as well as proliferation. The expression profile reported here provides a baseline against which changes of microglia in vitro can be examined. Importantly, expression profiling of normal microglia will help to provide the presently purely operational definition of ‘microglial activation’ with a molecular biological correlate. Furthermore, the data reported here add to our understanding of microglia biology and allow projections as to what functions microglia may exert in vivo, as well as in vitro.
DOI: 10.6084/m9.figshare.5104405
title: Supplementary Material for: Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome

description: Effective utilization of the domestic cat as an animal model for hereditary and infectious disease requires the development and implementation of high quality gene maps incorporating microsatellites and conserved coding gene markers. Previous feline linkage and radiation hybrid maps have lacked sufficient microsatellite coverage on all chromosomes to make effective use of full genome scans. Here we report the isolation and genomic mapping of 304 novel polymorphic repeat loci in the feline genome. The new loci were mapped in the domestic cat radiation hybrid panel using an automated fluorescent <i>Taq</i>-Man based assay. The addition of these 304 microsatellites brings the total number of microsatellites mapped in the feline genome to 580, and the total number of loci placed onto the RH map to 1,126. Microsatellites now span every autosome with an average spacing of roughly one polymorphic STR every five centimorgans, and full genome coverage of one marker every 2.7 megabases. These loci now provide a useful tool for undertaking full-genome scans to identify genes associated with phenotypes of interest, such as those relating to hereditary disease, coat color, patterning and morphology. These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses.