Physical mapping

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A standard cytogenetic map of Culex quinquefasciatus polytene chromosomes in application for fine scale physical mapping

A standard cytogenetic map of Culex quinquefasciatus polytene chromosomes in application for fine scale physical mapping

Special features of C. quinquefasciatus polytene chro- mosomes such as telomere fusions, ectopic contacts and extended length of chromosomal arms prevent a high yield of “readable” slides. So far, polytene chromosome preparation is not efficient on a large scale, which hin- ders whole-genome physical mapping using polytene chromosomes. Possibly, using mitotic chromosomes as a more easily and more reliably obtainable material could be a good complement to physical mapping on polytene chromosomes as it was demonstrated for the Aedes aegypti genome [31, 21] and C. quinquefasciatus genome [7]. Since the resolution of physical mapping using mi- totic chromosomes is approximately 10 times lower than that of polytene chromosomes, the mitotic chromo- somes could be used as a first step of the physical map- ping. Then in turn, polytene chromosomes can be utilized for the more detailed fine-scale mapping. Finally, these results can be combined and lead the complete or partial genome reassembly with correction of misassem- blies and connection of gaps. In the future, this iterative approach will lead to the construction of a high reso- lution physical map for C. quinquefasciatus genome and enable the creation of a more complete golden path file for this mosquito, and will be reflected in Vectorbase.
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Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs

Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs

to determine whether the probes shared enough homology species and may be used for fluorescent in situ hybridiza- to sorghum to effectively screen the BAC library. RFLP probes tion (FISH) to physically map a linkage group. This that passed prescreening tests were hybridized, as above, to a filter set (one copy of the library), using three probes simulta- approach to physical mapping has great potential in

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Physical mapping and complete nucleotide sequence of the denV gene of bacteriophage T4.

Physical mapping and complete nucleotide sequence of the denV gene of bacteriophage T4.

The physical mapping of the deletion endpoints in the T4farP12dC and T4farP13-dC mutants described above indicated that the rII-proximal left end of the denV gene must be located at a mo[r]

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Physical mapping studies of the X-linked agammaglobulinemia locus in Xq22

Physical mapping studies of the X-linked agammaglobulinemia locus in Xq22

There are at least five copies of the D X S lO l sequence in Xq22 (Hofkers et ah, 1987). Three of these have been isolated in cosmids. Probes were prepared from these cosmids which were representative of the three copies of D X S lO l that had been isolated. One proved to be too repetitive for use in long range physical mapping and was not pursued. Probes representative for the remaining two copies of the D X S lO l locus were both isolated and mapped. One was found to lie near to the DXS54 and PLP loci. Two studies have since been presented in which the order of the DXS54 and PLP loci have been mapped with respect to other loci in Xq22. O ’Reilly et al. (1993) place these two loci distal to the DXS94 and DXS 17 loci in the order: cen-PLP-DXS54-tel. This order and position was determined by the use of irradiation and fusion gene transfer (IFG T) hybrid cell lines and cannot be regarded as definitive as it is based on data from a single hybrid (O ’Reilly et al., 1993). Vetrie et al. (1993a) placed the DXS54 and PLP loci, and a copy of the D X S lO l locus assumed to be the same as the copy cloned here, proximal to the DXS94 locus, between the DXS 178 and DXS94 loci, in the order: cen- D X S 101 -DXS54-PLP-tel. This order was determined with YACs, and although a number of these YACs were chimeric (Vetrie et al., 1993a) this order seems likely to be correct. This places the copy of the D X S lO l locus recognised by the B550 probe approximately 2Mb distal to the DXS 178 locus. This copy is associated with the Eagl polymorphism described in chapter 4.
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Genetic and physical mapping in the terminal region of human chromosome 1p

Genetic and physical mapping in the terminal region of human chromosome 1p

recombinational hotspots in certain regions results in the inflation of genetic length. Where pre-existing genetic maps are used to guide physical mapping studies it is always wise to bear in mind the presence and possible effects of recombination hotspots and coldspots. Many examples exist which show a great deal of variation in the exact relationship of these two forms of measurement, which is often accounted for by their location along the chromosome. In studies of loci near centromeric regions, suppression of recombination has been noted, so called cold spots for recombination, which was noted for example, in chromosome 9 studies (Fountain et al, 1992). In distal regions where excess chiasma formation has been reported (Laurie et al, 1981; Laurie and Hulten, 1985) inflation of genetic distance is seen. In chromosome 21 for example, 50-100 kb were found to be equivalent to one cM between pairs of markers near the telomere (Burmeister et al, 1991b). Other reports illustrate a similar correlation, lcM=50kb; lcM=70kb, (Steinlein et al, 1992; Sefton et al, 1990). On the other hand an approximate one cM to one Mb relationship has been found in the cystic fibrosis maps (Drumm et al, 1988; Poutska et al, 1988). Reports of a disparity in order derived using physical and genetic mapping are very infrequent in the literature. Two examples however which show this are the studies on chromosome 20 (Steinlein et al, 1992) and on chromosome 13ql4 (Higgins et al, 1991). In the latter study for example, three markers were in the order: cen - D13S22 - D13S21 - D13S10 - tel, according to physical mapping studies. This order, however, was estimated to be 35000 times less likely in genetic mapping studies than the alternative order which inverted D13S22 and D13S21 (Higgins et al, 1990).
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Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice

Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice

A large chromosomal duplication involved in the dis- tal ends of rice chromosomes 11S and 12S: Two DNA markers, R1938 and R2918, were genetically mapped to the distal end of chromosome 11S, 0.5 and 1.9 cM from the marker S10637, respectively (Figure 1). These two markers were revealed to have their genomic copies also in the distal end of chromosome 12S by the present physical mapping (Figure 2). Marker C83, a cDNA clone showing strong homology to the ribosomal protein S25 and cosegregating with R2918, was judged to have four genomic copies according to its hybridization pattern with rice genomic DNA after DraI digestion, one of which, a 1.5-kb band, was confirmed from the YAC clone Y4889 on chromosome 11S. The second copy of this marker, a 3.7-kb band, was mapped to the long arm of chromosome 8. Although we were unable to determine the chromosomal locations of the remaining two geno- mic copies, it seemed that C83 had no copy in the duplicated region of chromosome 12S because it failed to hybridize to the YAC clones, Y2038, Y3404, and Y5335, that carried the genomic copy of R2918. Physical map- ping of other DNA markers located proximal to C83 revealed no homology between the two chromosomes (Shimokawa et al. 1996; Tanoue et al. 1997). These results indicated that the genomic area between the Figure 3.—Differences in the genetic distance of corre-
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Genetics and physical mapping studies on mouse chromosome 2

Genetics and physical mapping studies on mouse chromosome 2

The haploid gene content of the mouse and human genomes is thought to be very similar, approximately 80,000 genes (Antequera and Bird, 1993), although more conservative estimates have also been proposed (Fields at a!., 1994). Experience has shown that the majority of human genes have homologous sequences in the mouse genome (Copeland at a!., 1993). It is not clear how many of our genes have homologous (or orthoiogous) counterparts in the mouse genome, but the number of human genes with no mouse homologues will probably be very small. More importantly, as the genetic position of homologous DNA sequences is being determined in both species, it becomes apparent that many genes have retained their physical association in conserved linkage groups (Nadeau, 1989; O’Brien at a/., 1993; Copeland at a!., 1993). The extensive comparative maps now available provide an efficient way to predict the position of new genes on the human map by mapping them in the mouse. Conversely, the position of genes in the mouse genome can be predicted from mapping information in humans (e.g. Malas at a!., 1994). The expansion of the comparative map will primarily progress through genetic mapping, although some data from physical mapping will be necessary as the density of the map increases. In the mouse, genetic mapping is very powerful and very simple (see below). Hundreds or even thousands of genes can be mapped in multipoint crosses and the mapping information should be directly relevant to the human genome mapping effort (Copeland at a!., 1993). Strategies are now being initiated to maximise the efficiency and efficacy of the HGP by isolating and cataloguing all the genes in humans and mice. This represents a more efficient use of limited resources than the often more redundant effort to identify individual genes during existing research programs (Chapman at a!., 1993).
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On the Consistency of a Physical Mapping Method to Reconstruct a Chromosome in Vitro

On the Consistency of a Physical Mapping Method to Reconstruct a Chromosome in Vitro

An order estimation problem (16) based on the total linking distance is a stochastic optimization problem. The distribution of the linking distance DY will be ap- proxim[r]

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Molecular cloning and physical mapping of murine cytomegalovirus DNA.

Molecular cloning and physical mapping of murine cytomegalovirus DNA.

The results obtained after hybridization of 32P-labeled cloned fragments to Southern blots of MCMV DNA cleaved with HindIII, XbaI, EcoRI, BamHI, ApaI, ClaI, EcoRV, or KpnI allowed us to [r]

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Physical mapping of herpes simplex virus-induced polypeptides.

Physical mapping of herpes simplex virus-induced polypeptides.

The previously undescribed recombinants B x 5 7, B x 5 10, B x 6 17, 17+ x llr 1, and F x 5 12 were generated and plaque purified by the Downloaded from http://jvi.asm.org/ on November 1[r]

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Physical mapping of the human X chromosome

Physical mapping of the human X chromosome

Molecular biology is a fast moving field which has earned a great deal of attention in the past ten years since the first outline of the Human Genome Project was drawn up. It is a field that is concerned with answering questions related to human diseases, biological diversity and the functioning of the human body. It may even answer questions on brain functions, such as the biological basis for processes like memory. It is currently possible to relate various pieces of information and make deductions based on results that have been generated so far, although it is mostly restricted to very specialised questions, in specialised areas. For instance, the search for a biologically active molecule in the treatment of a monogenic disease can be considered as a relatively specialised problem. It is influenced by a limited number of factors, such as the possible interactions with the endogenous molecules involved in the metabolic pathway affected by the disease, and the secondary effects of candidate molecules etc. Another example is the search for a gene responsible for a monogenic disease. It follows one or more strategies but all are concemed with a very specific phenotype, set of patients, region of the genome, etc. Other questions however tackle more global problems or problems that have several causes that can not be separated from each other in the first place. An example is the mapping of polygenic diseases, such as hypertension and diabetes, which are caused by multiple genes interacting with each other and with environmental factors to create a gradient of susceptibility to the disease. Human geneticists confronted with such tasks must consider, measure and weigh a series of factors that span more than one field of biology, and take in account a large volume of data to obtain statistical significance. Another example is the analysis of protein function, once the corresponding gene has been identified and decoded. It will increasingly involve the comparison of protein sequences across many species for which representative model organisms have been studied in much greater detail than the human. With the recent publication of the complete sequence of the yeast genome, and the growing amount of characterised mutations in the bacteria, fruit fly, mouse or zebrafish this becomes increasingly possible. The colossal amounts of information that biologists have generated so far already makes answers to some of these complex questions a realistic prospect.
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Genetic and physical mapping of the short arm of human chromosome 9

Genetic and physical mapping of the short arm of human chromosome 9

polymorphisms (RFLPs) to construct a genetic linkage map of the human genome using the CEPH family DNA samples, which consisted of 403 markers. One limitation of RPLPs is that they are di-allelic and as such can only be, at most, heterozygous in 50% of the individuals investigated. In order to improve the information available, single locus probes for hypervariable loci (minisatellites) were developed (Wong et al, 1987), these probes were found to be most useful for DNA fingerprinting/profiling which is widely used in forensic laboratories. Two limitations of these probes in mapping were; Firstly, that the locus specific minisatellites appear to be non-randomly distributed in the genome, being clustered in the terminal band of a subset of chromosome arms (Wells et al, 1989, Vergnaud et al, 1993). Secondly, they have a high mutation rate compared to RFLPs or microsatellites, between 10 times (Jeffreys et al, 1985) and approximately 6 times (Jeffreys and Neumann, 1997) the rate seen in the rest of the genome . These limitations caused the minisatellites to be superseded as mapping tools by the advent of the polymerase chain reaction (PGR) and highly polymorphic microsatellite
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Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea.

Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea.

Mapping of telomeric restriction fragments: To eliminate possible telomeric rearrangements from affecting the linkage analysis, only progeny showing consistent segregation of[r]

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CLONING AND PHYSICAL MAPPING OF AN EARLY REGION OF THE BACTERIOPHAGE T4 GENOME

CLONING AND PHYSICAL MAPPING OF AN EARLY REGION OF THE BACTERIOPHAGE T4 GENOME

T o facilitate analysis of the gene 39-56 region, particularly the replication origin at 15.8 kb from the rZZA/rZZBjunction (coordinate 15.8), we have cloned Hind111 and [r]

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Physical mapping of adeno-associated virus serotype 4 DNA.

Physical mapping of adeno-associated virus serotype 4 DNA.

both enzymes produce a 320-base pair terminal fragment and is analyzed on 3 to 15% polyacrylamide gradient gels, submolar bands, which appear to represent the smaller terminal fragment, [r]

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Molecular cloning and physical mapping of the tupaia herpesvirus genome.

Molecular cloning and physical mapping of the tupaia herpesvirus genome.

Restriction maps for the restriction endonucleases EcoRI and Hindlll were constructed with data derived from Southern blot hybridizations of individual viral DNA fragments or cloned DNA [r]

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Genetic and Physical Mapping of Avr1a in Phytophthora sojae

Genetic and Physical Mapping of Avr1a in Phytophthora sojae

Markers cosegregating with Avr1a occur on an 170- kb BAC contig: To construct a physical map of the Avr1a region, markers closely linked to the gene were used as probes to screen a BAC library of P. sojae race 2 genomic DNA. A single BAC clone, 10-J14-1, was isolated using the AFLP marker HAMCGA as a probe. Fingerprinting of random BAC clones suggested that 10-J14-1, over- lapped with clones 3-M5-1, 17-C2-1, and 20-G5-1 (B. Tyler, unpublished data). This contig was confirmed by restriction mapping of the clones with the enzymes AseI, DraI, and NotI. Chromosome walking, using a probe derived from the T7 end of clone 10-J14-1, identified four new BAC clones, 31-A20-18, 23-H5-10, 36-M2-1, and 10- B21-7 (Figure 3). Overlapping regions were determined by restriction mapping and hybridization experiments, resulting in a physical contig of 170 kb. Besides the original marker used to screen the BAC library (CAP- CGA-3/4), none of the other markers shown in Figure 1 hybridized to any of the BAC clones in the extended contig. Thus, two new markers (10F1/3R2 and 10B21T7-2/5A) were developed along the contig for fine mapping of Avr1a.
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Genetic and Physical Mapping of the Mouse Ulnaless Locus

Genetic and Physical Mapping of the Mouse Ulnaless Locus

However, Ulnaless does not resemble the loss-of-func- tion phenotype in any of the Hoxa or Hoxd genes in the following respects: the intermediate elements of the limb (u[r]

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Characterization of the guinea pig cytomegalovirus genome by molecular cloning and physical mapping.

Characterization of the guinea pig cytomegalovirus genome by molecular cloning and physical mapping.

Gel-purified fragments were recleaved with the same restriction endonuclease used initially, placed again in a large well on a second agarose gel, reisolated, and used to prepare in vitr[r]

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Physical mapping of a large-plaque mutation of adenovirus type 2.

Physical mapping of a large-plaque mutation of adenovirus type 2.

Analysis of the recombinant DNAs by digestion with EcoRI or BamHI restriction endonucleases indicated that, as expected, recombination had occurred in overlapping sequences map position [r]

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