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  • 1
    Keywords: Human Genetics ; Human Genetics ; Springer eBooks
    Description / Table of Contents: Arthropod Genome Sequencing and Assembly Strategies -- Genome Size Estimation and Quantitative Cytogenetics in Insects -- Isolation of HMW DNA from Insects Chapter -- Long range sequencing and assembly QC -- Integrated modeling of structural genes using MCuNovo -- Using BUSCO to Assess Insect Genomic Resources -- The GFF3toolkit—QC and Merge Pipeline for Genome Annotation -- Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to identify functional regulatory DNA in insect genomes -- Using RAMPAGE to identify and annotate promoters in insect genomes -- CRM Beyond Model Insects -- Whole-genome bisulfite sequencing for the methylation analysis of insect genomes -- Bioinformatic analysis of methylation patterns using bisulfite sequencing data -- Physical Genome Mapping Using Fluorescence in Situ Hybridization with Mosquito Chromosomes -- Target enriched RAD sequencing (TEEseq): A new high-throughput sequencing approach applied to the comprehensive characterization of endosymbionts
    Abstract: This volume focuses on the latest methods used to sequence, assemble, and analyze insect genomes. The collection of protocols in this book provides an introduction to the workflows and bioinformatics tools available for researchers. The chapters cover a range of useful topics such as determining genome size by flow cytometry; High Molecular Weight DNA extraction; improvements to a genome assembly provided by long-range sequencing approaches; assessments of orthology and single-copy genes at different phylogenetic levels; detecting regulatory regions with FAIRE, RAMPAGE, and computational analysis of cis-regulatory modules in insects; bioinformatics analysis of epigenetic modifications, high-throughput scanning of insect genomes (TEEseq) for the presence of endosymbionts, and leveraging genome sequence information to design RNAi strategies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Insect Genomics: Methods and Protocols is a valuable resource for graduate students, postdocs, and novice research scientists who are interested in learning more about this developing field
    Pages: XI, 237 p. 34 illus., 23 illus. in color. : online resource.
    ISBN: 9781493987757
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  • 2
    ISSN: 1432-2072
    Keywords: A2 receptors ; Rotation ; Striatum ; Dopamine ; Apomorphine ; Rat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The effect of the purine agonist N-ethylcarboxamido-adenosine (NECA) on apomorphine-induced rotation was investigated in rats with unilateral 6-hydroxydopamine lesions of the nigrostriatal pathway. Intrastriatal administration of NECA on the denervated side caused a dose-dependent inhibition of contralateral rotation. This inhibition was prevented by prior intrastriatal injection of theophylline. The adenosine A1 receptor antagonist 8-cyclopentyltheophylline was ineffective at concentrations which block this receptor, but effective in preventing the action of NECA at concentrations which block the adenosine A2 receptor. In the absence of apomorphine, NECA had no effect on behaviour. It is concluded that A2 receptor activation counteracts apomorphine effects in the striatum. Since the A2 receptor may be localized to striatal cholinergic neurones, the possible role of these neurones in purine-induced behaviours is discussed.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-041X
    Keywords: Key words abdominal-A ; Homeotic selector gene ; Insect ; Morphological evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The Drosophila homeotic selector gene abdominal-A is important for determinative decisions in the anterior abdomen. Insects vary considerably with respect to abdominal morphology, and changes in the function of homeotic selector genes and/or downstream genes under their control presumably have been important to the evolution of these differences. Mutations in Abdominal, the Tribolium ortholog of abdominal-A, have been described, and have more posterior homeotic transformations than do Drosophila variants. Here we present the organization of the Abdominal gene and the sequences of its predicted proteins, the first such report for a non-Drosophilid insect. Two predicted proteins share N-terminal sequences with those proposed to be synthesized by the Drosophila ortholog. In addition, we describe the distribution of Abdominal transcripts during embryogenesis. The Tribolium expression pattern closely resembles that of Drosophila, and does not account for the differences in mutant phenotypes.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-041X
    Keywords: Key words orthodenticle ; Tribolium head development ; Homeobox gene ; Gene duplication ; Pattern formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  To investigate the molecular basis of head evolution, we searched for genes related to the Drosophila orthodenticle (otd) homeobox gene in the short-germ beetle Tribolium castaneum. Unexpectedly, we found that there are two otd-related genes in Tribolium, with predicted homeodomains highly similar to that of the single Drosophila gene. One of the two genes (Tc otd-1) is more related in both amino acid sequence and expression pattern to fruitfly otd. Tc otd-1 is expressed in a broad anterior stripe in the blastoderm embryo, suggesting a role in early head segmentation similar to that of the Drosophila gene. The second gene (Tc otd-2) is more similar in sequence to the otd-related genes isolated from different vertebrate species (the Otx gene family). Tc otd-2 is not transcribed in the blastoderm, but is expressed later in more limited subsets of cells in the anterior brain. Both Tribolium genes and the Drosophila gene are, unlike the vertebrate genes, also expressed at the developing ventral midline of the embryo. Our results are consistent with the idea that an otd/Otx gene specified anterior head structures in the last ancestor common to arthropods and vertebrates. Within the arthropod lineage, we propose that this gene acquired a function in cells at the developing midline prior to the duplication that generated the two Tribolium genes.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1432-041X
    Keywords: Key words Tribolium castaneum ; TGF-β superfamily ; Decapentaplegic ; Dorsal/ventral axis ; Appendage development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  We are characterizing members of the Transforming Growth Factor-β (TGF-β) superfamily in the red flour beetle, Tribolium castaneum, in order to examine the evolutionary conservation of the structure and function of TGF-β-like genes during insect development. A decapentaplegic-like gene of the TGF-β superfamily was isolated in Tribolium (Tc dpp) that is similar in sequence, organization, and expression to the Drosophila melanogaster dpp gene (Dm dpp). Conserved features include a high degree of sequence similarity in both the pro-domain and mature domains of the encoded polypeptide. In addition, the position of an intron within the protein-coding region is conserved in Tc dpp, Dm dpp, and two bone morphogenetic protein genes of the TGF-β superfamily in humans, BMP2 and BMP4. Consensus binding sites for the dorsal transcription factor are found within this intron in Tc dpp similar to the intronic location of several dorsal binding sites in Dm dpp. During embryogenesis, Tc dpp is expressed in an anterior cap of serosa cells at the blastoderm stage, in the dorsal ectoderm at the lateral edges of the developing and extended germ band, and in the distal tips of developing embryonic appendages. Several aspects of embryonic expression, similar in both flies and beetles, suggest conserved roles for dpp in cellular communication during the development of these distantly related insects.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-041X
    Keywords: Key words Ultrabithorax ; Ultrathorax ; Tribolium ; HOM-C ; Insect evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Ultrabithorax (Ubx) is essential for the proper patterning of the posterior thorax and anterior abdomen in Drosophila. The Coleoptera and Diptera differ in the organization and structure of their thorax and anterior abdomen. Changes in the regulation of Ubx and/or its downstream target genes are predicted to underlie these altered morphologies. We exploited the feasibility of genetic analysis in the red flour beetle, Tribolium castaneum, to examine the role of its Ubx ortholog in development. We analyzedgenomic and cDNA clones that predict a polypeptide with nearly 100% identity with the Drosophila Ubx gene in the homeodomain and flanking sequences. Southern blot analysis indicates that these clones represent DNA sequences within the Homeotic complex (HOM-C) of Tribolium. Phenotypic analysis of mutant variants of the Ultrathorax (Utx) gene, and its location within the beetle HOM-C, strongly supports Utx being the Tribolium ortholog of Ubx. The embryonic expression pattern of Ubx-homologous transcripts coincides with the phenotypes associated with Utx mutations, providing support that the Ubx-homologous cloned DNA represents the Utx locus. By mid-germband extension Utx transcripts are expressed in a pattern similar to Ubx in Drosophila. However, during early germband formation Utx transcripts differ in both spatial and temporal progression. Utx expression is initially detected in parasegments 4 and 5 (T1p–T3a) as they are established during early germband formation. This is the first report of the wild-type parasegmental expression of an insect Ubx ortholog extending through parasegment 4. The earlier and more anterior expression in the thorax may underlie the modification of the Coleopteran thorax.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0192-253X
    Keywords: Tribolium ; engrailed ; embryogenesis ; segmentation ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have cloned and sequenced the single Tribolium homolog of the Drosophila engrailed gene. The predicted protein contains a homeobox and several domains conserved among all engrailed genes identified to date. In addition it contains several features specific to the invected homologs of Bombyx and Drosophila, indicating that these features most likely were present in the ancestral gene in the common ancestor of holometabolous insects. We used the cross-reacting monoclonal antibody, 4D9, to follow the expression of the Engrailed protein during segmentation in Tribolium embryos. As in other insects, Engrailed accumulates in the nuclei of cells along the posterior margin of each segment. The first Engrailed stripe appears as the embryonic rudiment condenses. Then as the rudiment elongates into a germ band, Engrailed stripes appear in an anterior to posterior progression, just prior to morphological evidence of the formation of each segment. As in Drosophila (a long germ insect), expression of engrailed in Tribolium (classified as a short germ insect) is preceeded by the expression of several homologous segmentation genes, suggesting that similar genetic regulatory mechanisms are shared by diverse developmental types. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 0265-9247
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The powerful combination of genetic, developmental and molecular approaches possible with the fruit fly, Drosophila melanogaster, has led to a profound understanding of the genetic control of early developmental events. However, Drosophila is a highly specialized long germ insect, and the mechanisms controlling its early development may not be typical of insects or Arthropods in general. The beetle, Tribolium castaneum, offers a similar opportunity to integrate high resolution genetic analysis with the developmental/molecular approaches currently used in other organisms. Early results document significant differences between insect orders in the functions of genes responsible for establishing developmental commitments.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Abstract: The receptors responsible for the adenosine-mediated control of acetylcholine release from immunoaffinitypurified rat striatal cholinergic nerve terminals have been characterized. The relative affinities of three analogues for the inhibitory receptor were (R)-phenylisopropyladenosine > cyclohexyladenosine > N-ethylcarboxamidoadenosine (NECA), with binding being dependent of the presence of Mg2+ and inhibited by 5′-guanylylimidodiphosphate [Gpp(NH)p] and adenosine receptor antagonists. Adenosine A1 receptor agonists inhibited forskolin-stimulated cholinergic adenylate cyclase activity, with an IC50 of 0.5 nM for (R)-phenylisopropyladenosine and 500 nM for (S)-phenylisopropyladenosine. A1 agonists inhibited acetylcholine release at concentrations approximately 10% of those required to inhibit the cholinergic adenylate cyclase. High concentrations (1 μM) of adenosine A1 agonists were less effective in inhibiting both adenylate cyclase and acetylcholine release, due to the presence of a lower affinity stimulatory A2 receptor. Blockade of the A1 receptor with 8-cyclopentyl-1,3-dipropylxanthine revealed a half-maximal stimulation by NECA of the adenylate cyclase at 10 nM, and of acetylcholine release at approximately 100 nM. NECA-stimulated adenylate cyclase activity copurified with choline acetyltransferase in the preparation of the cholinergic nerve terminals, suggesting that the striatal A2 receptor is localized to cholinergic neurones. The possible role of feedback inhibitory and stimulatory receptors on cholinergic nerve terminals is discussed.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Abstract: Cholinergic nerve terminals were affinity purified from rat caudate nucleus. On stimulation with both 22.6 mM KCl and 50 μM veratridine, ATP was released in a Ca2+-dependent manner. The molar ratio of released acetyl-choline to ATP (9:1) was closer to that found in isolated cholinergic vesicles (7:1) than whole terminals (3:1). Extracellular [14C]ATP was rapidly metabolized by these terminals to adenosine and inosine via ectonucleotidases. The terminals had a saturable, high-affinity uptake mechanism for adenosine (Km= 16.6 μM). Veratridine stimulation also caused the Ca2+-dependent release of nucleosides in a dipyridamole-sensitive manner. Both theophylline treatment and inhibition of extracellular ATP breakdown resulted in increased ATP and nucleoside release. Extracellular adenosine was shown to inhibit acetylcholine release, probably via the Ai receptor. The role of extracellular purines at the cholinergic nerve terminal is discussed.
    Type of Medium: Electronic Resource
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