Toward a Physical Map of Drosophila buzzatii: Use of Randomly Amplified Polymorphic DNA Polymorphisms and Sequence-Tagged Site Landmarks

Abstract We present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z3 but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z3 had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed.

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Chromosomal Homology and Molecular Organization of Muller's Elements D and E in the Drosophila repleta Species Group

Genetics ◽

10.1093/genetics/145.2.281 ◽

1997 ◽

Vol 145 (2) ◽

pp. 281-295

Author(s):

José María ◽

Carmen Segarra ◽

Alfredo Ruiz

Keyword(s):

Polytene Chromosomes ◽

Species Group ◽

Molecular Organization ◽

Drosophila Genome ◽

Reciprocal Translocations ◽

Protein Coding ◽

Maximum Likelihood Procedure ◽

Positive Results ◽

Paracentric Inversions

Thirty-three DNA clones containing protein-coding genes have been used for in situ hybridization to the polytene chromosomes of two Drosophila repleta group species, D. repleta and D. buzzatii. Twenty-six clones gave positive results allowing the precise localization of 26 genes and the tentative identification of another nine. The results were fully consistent with the currently accepted chromosomal homologies and in no case was evidence for reciprocal translocations or pericentric inversions found. Most of the genes mapped to chromosomes 2 and 4 that are homologous, respectively, to chromosome arms 3R and 3L of D. melanogaster (Muller's elements E and D). The comparison of the molecular organization of these two elements between D. melanogaster and D. repleta (two species that belong to different subgenera and diverged some 62 million years ago) showed an extensive reorganization via paracentric inversions. Using a maximum likelihood procedure, we estimated that 130 paracentric inversions have become fixed in element E after the divergence of the two lineages. Therefore, the evolution rate for element E is approximately one inversion per million years. This value is comparable to previous estimates of the rate of evolution of chromosome X and yields an estimate of 4.5 inversions per million years for the whole Drosophila genome.

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A Physical Map of the Polytenized Region (101EF–102F) of Chromosome 4 in Drosophila melanogaster

Genetics ◽

10.1093/genetics/155.3.1175 ◽

2000 ◽

Vol 155 (3) ◽

pp. 1175-1183

Author(s):

John Locke ◽

Lynn Podemski ◽

Nicole Aippersbach ◽

Hilary Kemp ◽

Ross Hodgetts

Keyword(s):

Drosophila Melanogaster ◽

Physical Map ◽

Polytene Chromosomes ◽

Chromosome 4 ◽

Chromosome Walking ◽

Bac Clones ◽

Satellite Repeats ◽

Entry Points ◽

Minimal Tiling

Abstract Chromosome 4, the smallest autosome (~5 Mb in length) in Drosophila melanogaster contains two major regions. The centromeric domain (~4 Mb) is heterochromatic and consists primarily of short, satellite repeats. The remaining ~1.2 Mb, which constitutes the banded region (101E–102F) on salivary gland polytene chromosomes and contains the identified genes, is the region mapped in this study. Chromosome walking was hindered by the abundance of moderately repeated sequences dispersed along the chromosome, so we used many entry points to recover overlapping cosmid and BAC clones. In situ hybridization of probes from the two ends of the map to polytene chromosomes confirmed that the cloned region had spanned the 101E–102F interval. Our BAC clones comprised three contigs; one gap was positioned distally in 102EF and the other was located proximally at 102B. Twenty-three genes, representing about half of our revised estimate of the total number of genes on chromosome 4, were positioned on the BAC contigs. A minimal tiling set of the clones we have mapped will facilitate both the assembly of the DNA sequence of the chromosome and a functional analysis of its genes.

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Physical Map of the Malaria Vector Anopheles gambiae

Genetics ◽

10.1093/genetics/143.3.1307 ◽

1996 ◽

Vol 143 (3) ◽

pp. 1307-1311

Author(s):

A della Tome ◽

G Favia ◽

G Mariotti ◽

M Coluzzi ◽

K D Mathiopoulos

Keyword(s):

In Situ Hybridization ◽

Malaria Vector ◽

Nurse Cell ◽

Physical Map ◽

Polytene Chromosomes ◽

Chromosome Complement ◽

Cdna Clones ◽

Partial Nucleotide Sequence ◽

Small Set

Abstract Random cDNA clones, cosmid clones and RAPD polymorphic fragments have been localized by in situ hybridization to the ovarian nurse cell polytene chromosomes of the malaria vector Anopheles gambiue. We thus established 85 molecular markers for 110 sites within the whole A. gambiaepolytene chromosome complement. The cDNA clones analyzed were isolated at random, and their exact localizations were determined by in situ hybridization. For 15 of the cDNA clones, a partial nucleotide sequence has been obtained; for nine of them sequence searches in the GenBank database revealed high degrees of similarity with published sequences. The cosmid clones analyzed were obtained as the result of screening with a few of the aforementioned cDNA clones of particular interest, or taken from a small set of randomly isolated cosmid clones. The RAPD clones are polymorphic fragments, potentially diagnostic for the various chromosomal forms of A. gamhar that are currently being analyzed.

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Genetic mapping of Hessian fly avirulence gene vH6 using bulked segregant analysis

Genome ◽

10.1139/g98-071 ◽

1998 ◽

Vol 41 (5) ◽

pp. 702-708 ◽

Cited By ~ 10

Author(s):

J J Stuart ◽

S J Schulte ◽

P S Hall ◽

K M Mayer

Keyword(s):

In Situ Hybridization ◽

Bulked Segregant Analysis ◽

Polytene Chromosomes ◽

Hessian Fly ◽

Mayetiola Destructor ◽

Dna Polymorphisms ◽

Avirulence Gene ◽

Conformational Polymorphism ◽

Single Stranded Conformational Polymorphism

The Hessian fly, Mayetiola destructor (Say), an important insect pest of wheat, Triticum aestivum L., has a gene-for-gene relationship with wheat: single genes in the insect condition avirulence to specific resistance genes in wheat. We report the discovery of the first molecular genetic marker that is tightly linked to a Hessian fly avirulence gene. This dominant DNA polymorphism (OPG15-1) was identified using bulked segregant analysis and arbitrary primers in polymerase chain reactions. Bulked segregant analysis was modified to accommodate the anomalous chromosome cycle of the Hessian fly. It was used to identify DNA polymorphisms linked to the gene (vH6) that confers avirulence to the resistance gene H6 in wheat. OPG15-1 was cloned and sequenced, and a pair of site-specific primers were designed that converted it into a codominant single-stranded conformational polymorphism. Both OPG15-1 and vH6 were shown to be X-linked, and the genetic distance between the two loci was 2.5 ± 2.5 cM. In situ hybridization to polytene chromosomes of larval salivary glands indicated that OPG15-1 resides near the centromere of Hessian fly chromosome X1.Key words: Mayetiola destructor, avirulence gene, RAPD-PCR, bulked segregant analysis, single-stranded conformational polymorphism, SSCP, in situ hybridization.

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Integrated Genetic Map of Anopheles gambiae: Use of RAPD Polymorphisms for Genetic, Cytogenetic and STS Landmarks

Genetics ◽

10.1093/genetics/143.2.953 ◽

1996 ◽

Vol 143 (2) ◽

pp. 953-960

Author(s):

George Dimopoulos ◽

Liangbiao Zheng ◽

Vasantha Kumar ◽

Alessandra della Torre ◽

Fotis C Kafatos ◽

...

Keyword(s):

Anopheles Gambiae ◽

Polytene Chromosomes ◽

Sequence Tagged Sites ◽

Entry Points ◽

Vector Mosquito ◽

Mosquito Anopheles Gambiae ◽

Generating Sequence ◽

Integrated Genetic Map ◽

Gambiae Genome

Abstract Randomly amplified polymorphic DNA (RAPD) markers have been integrated in the genetic and cytogenetic maps of the malaria vector mosquito, Anopheles gambiae. Fifteen of these markers were mapped by recombination, relative to microsatellite markers that had been mapped previously. Thirty-four gel-purified RAPD bands were cloned and sequenced, generating sequence tagged sites (STSs) that can be used as entry points to the A. gambiae genome. Thirty one of these STSs were localized on nurse cell polytene chromosomes through their unique hybridization signal in in situ hybridization experiments. Five STSs map close to the breakpoints of polymorphic inversions, which are notable features of the Anopheles genome. The usefulness and limitations of this integrated mosquito map are discussed.

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The evolutionary history of Drosophila buzzatii. XXIII. High content of nonsatellite repetitive DNA in D. buzzatii and in its sibling D. koepferae

Genome ◽

10.1139/g92-148 ◽

1992 ◽

Vol 35 (6) ◽

pp. 967-974 ◽

Cited By ~ 6

Author(s):

I. Marin ◽

M. Labrador ◽

A. Fontdevila

Keyword(s):

Repetitive Dna ◽

Sibling Species ◽

Genomic Dna ◽

Repetitive Sequences ◽

Polytene Chromosomes ◽

Drosophila Buzzatii ◽

Repleta Group ◽

Wide Variability ◽

History Of

The frequency and types of repetitive nonsatellite DNA of two sibling species of the repleta group of Drosophila, D. buzzatii, and D. koepferae have been determined. For each species, the analysis is based on a sample of more than 100 clones (400 kb) obtained from genomic DNA. A theoretical model has been developed to correct for the presence of a mixture of repetitive and unique DNA in these clones. After correction, a high content of repetitive DNA has been demonstrated for both species (D. buzzatii, 19–26%; D. koepferae, 27–32%). The repetitive sequences have been classified according to their hybridization pattern when used as probes against genomic DNA and by their in situ hybridization signals on polytene chromosomes. Data suggest that the main nonsatellite component of these species is simpler and more repetitive than that of D. melanogaster, pointing to a wide variability in content and class size distribution of repetitive DNA among Drosophila species.Key words: repetitive DNA, DNA evolution, Drosophila, repleta group, sibling species.

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NIR responsive tumor vaccine in situ for photothermal ablation and chemotherapy to trigger robust antitumor immune responses

Journal of Nanobiotechnology ◽

10.1186/s12951-021-00880-x ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Lirong Zhang ◽

Jingjing Zhang ◽

Lixia Xu ◽

Zijian Zhuang ◽

Jingjin Liu ◽

...

Keyword(s):

Immune Responses ◽

Tumor Vaccine ◽

Oxidative Polymerization ◽

Delivery Mode ◽

Tumor Treatment ◽

One Pot ◽

Photothermal Ablation ◽

Prolonged Retention ◽

The One

Abstract Background Therapeutic tumor vaccine (TTV) that induces tumor-specific immunity has enormous potentials in tumor treatment, but high heterogeneity and poor immunogenicity of tumor seriously impair its clinical efficacy. Herein, a novel NIR responsive tumor vaccine in situ (HA-PDA@IQ/DOX HG) was prepared by integrating hyaluronic acid functionalized polydopamine nanoparticles (HA-PDA NPs) with immune adjuvants (Imiquimod, IQ) and doxorubicin (DOX) into thermal-sensitive hydrogel. Results HA-PDA@IQ NPs with high photothermal conversion efficiency (41.2%) and T1-relaxation efficiency were using HA as stabilizer by the one-pot oxidative polymerization. Then, HA-PDA@IQ loaded DOX via π-π stacking and mixed with thermal-sensitive hydrogel to form the HA-PDA@IQ/DOX HG. The hydrogel-confined delivery mode endowed HA-PDA@IQ/DOX NPs with multiple photothermal ablation performance once injection upon NIR irradiation due to the prolonged retention in tumor site. More importantly, this mode enabled HA-PDA@IQ/DOX NPs to promote the DC maturation, memory T cells in lymphatic node as well as cytotoxic T lymphocytes in spleen. Conclusion Taken together, the HA-PDA@IQ/DOX HG could be served as a theranostic tumor vaccine for complete photothermal ablation to trigger robust antitumor immune responses.

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Molecular Characterization of hobo-Mediated Inversions in Drosophila melanogaster

Genetics ◽

10.1093/genetics/144.2.647 ◽

1996 ◽

Vol 144 (2) ◽

pp. 647-656

Author(s):

William B Eggleston ◽

Nac R Rim ◽

Johng K Lim

Keyword(s):

X Chromosome ◽

Polymerase Chain Reaction Amplification ◽

Polytene Chromosomes ◽

Chromosomal Inversions ◽

Hobo Element ◽

Reaction Amplification ◽

Notch Locus ◽

Polymerase Chain

Abstract The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation.

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CHROMOSOMAL SEQUENCES AND INTERISLAND COLONIZATIONS IN HAWAIIAN DROSOPHILA

Genetics ◽

10.1093/genetics/103.3.465 ◽

1983 ◽

Vol 103 (3) ◽

pp. 465-482

Author(s):

Hampton L Carson

Keyword(s):

Polytene Chromosomes ◽

Complex Species ◽

Hawaiian Drosophila ◽

On This Island ◽

Break Points ◽

Chromosomal Sequences ◽

Founder Events ◽

Paracentric Inversions ◽

Single Set

ABSTRACT Of 103 picture-winged Drosophila species endemic to the high Hawaiian islands, all but three are endemic to single islands or island complexes. They are presumed to have evolved in situ on each island. The banding pattern sequences of the five major polytene chromosomes of these species have been mapped to a single set of Standard sequences. Sequential variation among these chromosomes is due to 213 paracentric inversions. An atlas of their break points is provided. Geographical, morphological and behavioral data may be used to supplement the cytological information in tracing ancestry. Starting at the newer end of the archipelago, the 26 species of the Island of Hawaii (less than 700,000 years old) are inferred to have been derived from 19 founders, 15 from the Maui complex, three from Oahu and one from Kauai. The existence of 40 Maui complex species is explicable as resulting from 12 founders, ten from Oahu and two from Kauai. The 29 Oahu species can be explained by 12 founder events, five from Kauai and seven from Maui complex (summary in Figure 5). Although the ancestry of two Kauai species can be traced to newer islands, the ten remaining ones on this island (age about 5.6 million years) are apparently ancient elements in the fauna, relating ultimately to Palearctic continental sources.

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A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites.

Genetics ◽

10.1093/genetics/131.3.609 ◽

1992 ◽

Vol 131 (3) ◽

pp. 609-624 ◽

Cited By ~ 13

Author(s):

B D Williams ◽

B Schrank ◽

C Huynh ◽

R Shownkeen ◽

R H Waterston

Keyword(s):

Caenorhabditis Elegans ◽

Genetic Mapping ◽

Physical Map ◽

Nematode Caenorhabditis Elegans ◽

C Elegans ◽

Sequence Tagged Sites ◽

Mapping System ◽

Polymerase Chain ◽

Tc1 Element ◽

Single Reaction

Abstract We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol "empty" site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross.

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