Physical Map

The Schizosaccharomycespombe centromere- linked genes, LYS] and CYHI on chromosome I and TPS13 and RAN) on chromosome II, have been isolated. The genetic order of these markers with respect to their centromeres was deter- mined to establish relative directionality on the genetic and physical maps. Chromosome walking toward the centromeres reveals a group of repetitive sequences that occur only in the centromere regions of chromosomes I and II and at one other specific location in the S. pombe genome, presumably the centromere of chromosome ITH. The major class of large repeated sequence elements is 6.4 kilobases (kb) long (repeat K), portions ofwhich occur at least twice on chromosome II and in several tandemly arranged intact copies at another centromeric location. Repeat K in turn contains groups of smaller repeats. Genetic recombination is strongly suppressed in the centromere II region, which contains at least 30 kb of repeated sequences. Centromeric DNA organization is much more complex in fission yeast than has been described in budding yeast (Saccharomyces cerevisiae), possibly because of the larger more condensed nature of the S. pombe chromosomes.

An interactive graphic viewer, ChromoScope, was developed to explore scientific visualization of complicated genome data. Escherichia c o 1 i was selected as the test organism. An ASN.l data set has been built for the entire E . coli chromosome, including a genetic map, a physical (ordered restriction) map, the alignment between the two maps, Kohara clones and some short repeat features. The E. coli sequence is modeled as a segmented sequence, incorporating both the sequence and the physical map data. The alignment between the contig and the published sequences is stored as sequence history, allowing direct access to the same sequence in the public databases. The alignment is displayed graphically, with both the sequence alignment and feature annotations. The alignment viewer also supports a detailed text display, providing information to resolution at residue level with annotated features.

SUMMARY A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.

Acquired interstitial loss of all or part of the long arm of human chromosome 5 (5q-) is an anomaly that is seen frequently in patients with preleukemic myelodysplasia and acute myelogenous leukemia. Loss of a critical region of overlap at band 5q31.1 in all of these cases, with various cytogenetic breaks, signifies the existence of a key negative regulator of leukemogenesis. Previous studies have defined the proximal and distal ends of the critical region to reside between the genes for IL9 and EGR1, respectively. In this report, we describe a yeast artificial chromosome contig spanning this myeloid tumor suppressor locus. The combined order of the polymorphic loci is centromere-IL9-(D5S525-D5S558-D5S89-D5S526 -D5S393)-D5S399-D5S396-D5S414-EGR1 and telomere. The physical distance between the IL9 and EGR1 genes is estimated to be < 2.4 Mb. Here we report the utility of these polymorphic loci by detecting a submicroscopic deletion of 5q31; an acute myelogenous leukemia patient wit...

Understanding of the human genome has been advanced significantly by the development of large DNA fragment libraries. To create a map of chromosome 21q that integrates the physical, cytogenetic, and linkage maps, we have characterized a subset of 127 chromosome 21 yeast artificial chromosome (YAC) clones for size, by pulsed field gel electrophoresis, for chimerism and cytogenetic location, by fluorescence in situ hybridization (FISH), and for sequence-tagged sites (STS) content, by PCR. It was found that 54% generated unique map locations on chromosome 21, and 45% detected sites on other chromosomes, of which 33% likely represented true chimerism. Using a simple algorithm, the data from nonchimeric clones have been combined to generate a size-corrected minimal tiling pathway including 58 chromosome 21q YACs that represent approximately 33 Mb and include 9 gaps. To confirm the resulting order and relationship to the cytogenetic map, the breakpoints from 23 cell lines partially aneupl...

Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this research were to develop new primers flanking wheat microsatellites and to position the associated loci on the wheat genome map by genetic linkage mapping in the ITMI W7984 • Opata85 recombinant inbred line (RIL) population and/or by physical mapping with cytogenetic stocks. We observed that the efficiency of marker development could be increased in wheat by creating libraries from sheared rather than enzyme-digested DNA fragments for microsatellite screening, by focusing on microsatellites with the [ATT/TAA] n motif, and by adding an untemplated G-C clamp to the 5¢-end of primers. A total of 540 microsatellite-flanking primer pairs were developed, tested, and annotated from ran-dom genomic libraries. Primer pairs and associated loci were assigned identifiers prefixed with BARC (the acronym for the USDA-ARS Beltsville Agricultural Research Center) or Xbarc, respectively. A subset of 315 primer sets was used to map 347 loci. One hundred and twenty-five loci were localized by physical mapping alone. Of the 222 loci mapped with the ITMI population, 126 were also physically mapped. Considering all mapped loci, 126, 125, and 96 mapped to the A, B, and D genomes, respectively. Twenty-three of the new loci were positioned in gaps larger than 10 cM in the map based on pre-existing markers, and 14 mapped to the ends of chromosomes. The length of the linkage map was extended by 80.7 cM. Map positions were consistent for 111 of the 126 loci positioned by both genetic and physical mapping. The majority of the 15 discrepancies between genetic and physical mapping involved chromosome group 5.

Mycoplasma synoviae, a major pathogen of poultry, contains a single expressed, full-length vlhA gene encoding its haemagglutinin, and a large number of vlhA pseudogenes that can be recruited by multiple site-specific recombination events to generate chimaeric variants of the expressed gene. The position and distribution of the vlhA pseudogene regions, and their relationship with the expressed gene, have not been investigated. To determine the relationship between these regions, a physical map of the M. synoviae genome was constructed using the restriction endonucleases SmaI, I-CeuI, Bsi WI, ApaI and XhoI and radiolabelled probes for rrnA, recA and tufA. A cloned fragment encoding the unique portion of the expressed vlhA gene and two PCR products containing conserved regions of the ORF 3 and ORF 6 vlhA pseudogenes were used to locate the regions containing these genes on the map. The chromosome of M. synoviae was found to be 890?4 kb and the two rRNA operons were in the same orientation. Both the expressed vlhA gene and the vlhA pseudogenes were confined to the same 114 kb region of the chromosome. These findings indicate that, unlike Mycoplasma gallisepticum, in which the vlhA genes are located in several loci around the chromosome and in which antigenic variation is generated by alternating transcription of over 40 translationally competent genes, M. synoviae has all of the vlhA sequences clustered together, suggesting that close proximity is needed to facilitate the site-specific recombinations used to generate diversity in the expressed vlhA gene.

In order to take into account physical design effects, a designer needs a feedback mechanism during interactive data path synthesis. In this paper, we propose a hypergraph model and a back-annotation algorithm which provide a feedback mechanism for back-annotation from physical designs to behavioral descriptions. Given a control-data flow graph and its structural design, this back-annotation technique can not only evaluate the design quality but can also feedback the delay to each edge and node in the graph. Therefore, a designer can identify the critical paths and improve the design. The hypergraph model and the back-annotation algorithm allow us to bridge the gap between the behavioral description and the physical design.

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350–base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.

Changes in the global climate pose a danger to plant growth and production and have a significant direct and indirect impact on the quantity and quality of plant nutrients. Combined with the rise in abiotic stresses, notably drought, developing nations are in urgent need of solutions that will maintain the production and nutritive value of their food crops. An essential food and oil crop for the world, groundnut supports agriculturally based livelihood methods that ensure food, nutrition, and financial security. Groundnut is an energy-dense food item and it contains a substantial amount of fat, proteins, and carbohydrates both fat soluble and water soluble vitamins, fibers, polyphenols, antioxidants, vitamins, and minerals. Due to the high nutrient contents of peanuts, they have been used to combat malnutrition in most developing countries.India is the second largest producer of groundnuts in the world, and the crop's primary usage is for its oil. Peanuts are consumed in many forms such as boiled peanuts, peanut oil, peanut butter, roasted peanuts, and added peanut meal in snack food, energy bars, and candies.Drought causes substantial yield losses to groundnut production and adversely impacts nutritional quality. Increased aflatoxin levels in groundnuts during field production are caused, in part, by drought stress, which limits the use of peanuts as healthy food and has a negative influence on the peanut trade.Therefore, maintaining groundnut nutritional quality under drought stress may present a great opportunity to supply enough human food and animal feed. This article focuses on the impact of drought stress on the nutritional value of groundnuts and provides an overview of the nutritional chemistry of groundnut components in relation to health benefits.

Holeta has different peach fruit varieties that can be used for various purposes. However, their fruit quality characteristics were not fully identified. Studies have indicated that the physicochemical qualities of peach fruits are influenced by a number of factors, with the varietal factor being one of the most important. Limited information regarding the factors that affect these qualities is available in the country, specifically at Holeta. Therefore, this study was initiated to evaluate the physicochemical quality properties of peach fruit varieties. Their physical quality traits, such as fruit length, fruit diameter, fruit shape index, and average fruit weight, as well as chemical quality parameters, such as TSS, specific gravity, TA, ripening index, ascorbic acid content, and pH, were evaluated. The results revealed that both physical and chemical quality parameters were significantly affected by varietal factors. Among cultivars, 'Bonny Gold' had the longest fruit length, and 'Florida Down' had the largest fruit diameter. As far as average fruit weight is concerned, 88-18 W had the highest weight with 111.98 g, while Transvalia had the highest TSS and specific gravity. However, the 'Summer Sun' and 9A-35C varieties had the highest TA and ripening index, respectively. Thus, the physicochemical quality properties of the fruit were highly altered with peach varieties. Cuvinte cheie: fruct, fizico-chimic, calitate, soiuri, SST, AT, index de maturare.

Background Self-incompatibility (SI) is a physiological mechanism that many flowering plants employ to prevent self-fertilization and maintain heterozygosity. In the grass family this is known to be controlled by a two locus (S-Z) system; however, the SI system is intrinsically leaky. Modifier genes of both the S and Z loci and a further locus, T, are known to override SI leading to self-fertilization and self-seed production. This has implications for the ecological and evolutionary success as well as the commercial breeding of grasses. Here we report a study where the genetic control of self-compatibility (SC) was determined from the results of self-pollinating an F 2 population of perennial ryegrass from two independently derived inbred lines produced by single-seed descent. • Methods In vitro self-pollinations of 73 fertile plants were analysed. A genetic association analysis was made with a panel of 1863 single-nucleotide polymorphism (SNP) markers, generated through genotype-by-sequencing methodology. Markers were placed on a recombination map of seven linkage groups (LGs) created using Joinmap v.5. The seed set on self-and open-pollinated inflorescences was determined on 143 plants, including the 73 plants analysed for self-pollination response. • Key Results Self-pollinations revealed a bimodal distribution of percentage SC with peaks at 50 and 100 %. A single quantitative trait locus (QTL) was identified with peak association for marker 6S14665z17875_11873 that mapped to LG 6. Peak position was associated with maximum marker segregation distortion. The self-compatible plants were equally fecund after self-and open pollination. • Conclusions This is the first report in the Poaceae family of an SC locus located on LG 6. This new SC QTL discovery, as well as indicating the complex nature of the pollen-stigma recognition process and its evolutionary significance, provides an additional source of SC for breeding perennial ryegrass.

BackgroundSelf-incompatibility (SI) is a physiological mechanism that many flowering plants employ to prevent self-fertilization and maintain heterozygosity. In the grass family this is known to be controlled by a two locus (S-Z) system; however, the SI system is intrinsically leaky. Modifier genes of both the S and Z loci and a further locus, T, are known to override SI leading to self-fertilization and self-seed production. This has implications for the ecological and evolutionary success as well as the commercial breeding of grasses. Here we report a study where the genetic control of self-compatibility (SC) was determined from the results of self-pollinating an F2 population of perennial ryegrass from two independently derived inbred lines produced by single-seed descent.MethodsIn vitro self-pollinations of 73 fertile plants were analysed. A genetic association analysis was made with a panel of 1863 single-nucleotide polymorphism (SNP) markers, generated through genotype-by-sequ...

. We gratefully acknowledge grants K01-HG00055 (to D.G.), HG00008 (to J.O.), K05 CA90754 (to E.A.O.), and R01 CA92167 (to E.A.O.). M. B. Corwin was supported by the Hebrew Technical Institute as part of the Rockefeller University Summer Outreach Program. C. S. Mellersh was funded by a postdoctoral fellowship from Ralston Purina. E. A. Ostrander also gratefully acknowledges the support of the American Kennel Club Canine Health Foundation and a Burroughs Wellcome Award for Excellence in Functional Genomics. We thank Gregory Acland and Gustavo Aguirre for use of the ERD data and Thora Jonasdottir, Lars Moe, and Frode Lingaas for use of the RCND data set. We also thank anonymous reviewers for helpful comments. This paper was delivered at the Advances in Canine and Feline Genomics symposium,

The unc‐47 locus of Caenorhabditis elegans has been suggested to encode a synaptic vesicle GABA transporter. Here we used hydropathy plot analysis to identify a candidate vesicular GABA transporter in genomic sequences derived from a region of the physical map comprising unc‐47. A mouse homologue was identified and cloned from EST database information. In situ hybridization in rat brain revealed codistribution with both GABAergic and glycinergic neuronal markers. Moreover, expression in COS‐7 and PC12 cells induced an intracellular, glycine‐sensitive GABA uptake activity. These observations, consistent with previous data on GABA and glycine uptake by synaptic vesicles, demonstrate that the mouse clone encodes a vesicular inhibitory amino acid transporter.

pigmentation pattern of the species ( Figure 1C,D;. There is, however, a range of phenotypes exhibited by snakes possessing Sa and Ss alleles. Primarily affected are the size and pattern of dorsal and lateral body blotches, and the degree to which melanin is expressed in scales. Undoubtedly pigmentation pattern in Sa and Ss individuals is influenced by modifiers and/or the environment. Future work includes performing crosses between individuals possessing both the salmon (Sa and Ss) and albinism (Al) trait, and those that are homozygotes, Ss ϫ Ss. It is known that the Sa trait we report in captive B. constrictor occurs in certain populations from Panama (Porras 1999; Hardy D Sr, personal communication). According to Porras (1999, personal communication), B. constrictor from Isla Taboguilla ( Bahia de Panama) show the Sa trait (p. 60), and some individuals bear a strong resemblance to the Ss phenotype (pp. 51-52). D. Hardy, Sr. (personal communication) collected a juvenile female B. constrictor from the region of Gamboa, Panama, that showed the Sa condition. Because we have limited information on the Sa trait in B. constrictor, the extent of its geographic distribution remains to be established. Nonetheless, at present we are aware of no other localities than those provided above (Porras L, personal communication), and thus tentatively conclude that the Sa mutation has a limited geographic distribution in B. constrictor. Of importance, these data provide information that will be of utility to systematists and taxonomists working on this species. Based on our findings, populations of B. constrictor expressing the Sa or Ss pigmentation pattern should not be considered as distinct geographic races or other type of evolutionary unit. Rather it is our opinion that these populations show polymorphism with respect to pigmentation pattern.

The construction of a physical map of chromosome 4H ch from Hordeum chilense containing molecular markers capable of detecting segments of this chromosome in a wheat background would be very useful for marker-assisted introgression of 4H ch chromatin into both durum and common wheat. With this aim, the applicability of 106 barley chromosome 4H primers (62 SSRs and 44 STSs) to amplify markers showing polymorphism between H. chilense and both common or bread and durum wheat was investigated. Twenty-Wve SSR (40.3%) and six STS (13.6%) barley primer pairs consistently ampliWed H. chilense products. Eight SSR (12.9%) and four STS (9.1%) barley primers were polymorphic between H. chilense and both common and durum wheat, 10 of them (6 SSRs and 4 STSs) were located on chromosome 4H ch using both the addition line of chromosome 4H ch in Chinese Spring wheat and a tritordeum line (an amphiploid between H. chilense and T. turgidum) nullisomic for chromosome 4H ch . Additionally, 18 EST-SSR barley markers previously located on chromosome 4H ch were screened for polymorphism; 15 were polymorphic between H. chilense and both durum and common wheat. For physical mapping we used a ditelosomic tritordeum line for the short arm of chromosome 4H ch and a tritordeum line homozygous for a 70% terminal deletion of the long arm of 4H ch . A total of 25 markers (6 SSRs, 4 STSs and 15 EST-SSRs) were mapped to chromosome 4H ch . Eight markers were allocated on the 4H ch S, eight were mapped in the 30% proximal region of 4H ch L and nine were on the 70% distal region of 4H ch L, respectively. Arm location on barley chromosome 4H was also carried out using both 4HS and 4HL ditelosomic addition lines in wheat. All markers mapped may have a role in marker-assisted introgression of chromatin segments of chromosome 4H ch in both durum and common wheat backgrounds.

▼PCR-based screenings of DNA or spheroplasts from individual clones or pools have proven to be efficient for identification of gene-specific clones within YAC contigs (Ref. 1). While colony-PCR-based methods have been shown to be simple, rapid and efficient approaches for screening individual recombinant bacterial colonies, conflicting data concerning the application of colony-PCR-based screenings of YAC clones have been published (Ref. 2,. Two papers showed that PCR can be performed on yeast cells without extensive DNA extractions, using whole yeast cells or spheroplasts as templates for PCR (Ref. 2, 3), while a third report states that colony-PCR procedures are ineffective for yeast cells (Ref. 4). Data presented here demonstrate that inoculates of whole cells, from solid plates and from liquid cultures, are satisfactory templates in PCR reactions, at least when amplified fragments are relatively short

In an edge-colored graph, the cost incurred at a vertex on a path when two incident edges with different colors are traversed is called reload or changeover cost. The Minimum Changeover Cost Arborescence (MinCCA) problem consists in finding an arborescence with a given root vertex such that the total changeover cost of the internal vertices is minimized. It has been recently proved by Gözüpek et al. [14] that the MinCCA problem is FPT when parameterized by the treewidth and the maximum degree of the input graph. In this article we present the following results for MinCCA: • the problem is W[1]-hard parameterized by the treedepth of the input graph, even on graphs of average degree at most 8. In particular, it is W[1]hard parameterized by the treewidth of the input graph, which answers the main open problem of [14]; • it is W[1]-hard on multigraphs parameterized by the tree-cutwidth of the input multigraph; • it is FPT parameterized by the star tree-cutwidth of the input graph, which is a slightly restricted version of tree-cutwidth. This result strictly generalizes the FPT result given in [14]; • it remains NP-hard on planar graphs even when restricted to instances with at most 6 colors and 0/1 symmetric costs, or when restricted to instances with at most 8 colors, maximum degree bounded by 4, and 0/1 symmetric costs.

Background We have initiated an effort to exhaustively map interactions between HTLV-1 Tax and host cellular proteins. The resulting Tax interactome will have significant utility toward defining new and understanding known activities of this important viral protein. In addition, the completion of a full Tax interactome will also help shed light upon the functional consequences of these myriad Tax activities. The physical mapping process involved the affinity isolation of Tax complexes followed by sequence identification using tandem mass spectrometry. To date we have mapped 250 cellular components within this interactome. Here we present our approach to prioritizing these interactions via an in silico culling process. Results We first constructed an in silico Tax interactome comprised of 46 literature-confirmed protein-protein interactions. This number was then reduced to four Tax-interactions suspected to play a role in DNA damage response (Rad51, TOP1, Chk2, 53BP1). The first-neig...

Genome sequences for most metazoans and plants are incomplete because of the presence of repeated DNA in the heterochromatin. The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. We describe the generation of 15 Mb of finished or improved heterochromatic sequence with the use of available clone resources and assembly methods. We also constructed a bacterial artificial chromosome–based physical map that spans 13 Mb of the pericentromeric heterochromatin and a cytogenetic map that positions 11 Mb in specific chromosomal locations. We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans.

A physical map has been constructed of the human genome containing 15,086 sequencetagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 6193 loci and incorporated a genetic linkage map of the human genome containing 5264 loci. This information was combined with the results of STS-content screening of 10,850 loci against a yeast artificial chromosome library to produce an integrated map, anchored by the radiation hybrid and genetic maps. The map provides radiation hybrid coverage of 99 percent and physical coverage of 94 percent of the human genome. The map als0 represents an early step in an international project to generate a transcript map of the human genome, with more than 3235 expressed sequences localized. The STSs in the map provide a scaffold for initiating large-scale sequencing of the human genome.

Deletions of the long arm of chromosome 20 have been reported in a wide range of myeloid disorders and may re¯ect loss of critical tumor suppressor gene(s). To identify such candidate genes, 65 human myeloid cell line DNAs were screened by polymerase chain reaction (PCR) for evidence of allelic loss at 39 highly polymorphic loci on the long arm of chromosome 20. A mono-allelic pattern was present in eight cell lines at multiple adjacent loci spanning the common deleted regions (CDRs) previously de®ned in primary hematological samples, suggesting loss of heterozygosity (LOH) at 20q. Fluorescence in situ hybridization (FISH) was then performed using a series of yeast arti®cial chromosomes (YACs) ordered in the CDR, and in ®ve of eight cell lines, the deletions resulted from cytogenetically detectable whole chromosomal loss or large interstitial deletion, whereas in another cell line deletion was associated with an unbalanced translocation. LOH in the CMK megakaryocytic cell line, which has a hypotetraploid karyotype, was associated with a der(20)t(1;20)(q32;q12)x2 leading to complete deletion of the CDR. Three additional unbalanced translocations were found within the CDR and all three breakpoints mapped to a single YAC. We then used a series of P1 arti®cial chromosomes (PACs) spanning this YAC clone, and two PACs produced `split' signals suggesting that they each span one of these breakpoints. Exon trapping using PACs that overlap the breakpoint regions yielded portions of six genes and evaluation of these genes as candidate tumor suppressor genes is underway. The limited information available about these genes suggests that the h-l(3)mbt gene is the most attractive candidate. Oncogene (2001) 20, 4150 ± 4160.

material was correlated with loss of androgen respon-Numerous studies have implicated the short arm of siveness (Konig et al., 1989). Since then, subregional chromosome 8 as the site of one or more tumor supdeletion analysis of chromosome 8p in prostate cancer pressor genes inactivated in carcinogenesis of the has been performed by a number of groups using a prostate, colon, lung, and liver. Previously, we identivariety of molecular methods, all of which have confied a homozygous deletion on chromosome 8p22 in a firmed a high frequency of loss in this region, especially metastatic prostate cancer. To map this homozygous but not exclusively within chromosome band 8p22 (Berdeletion physically, long-range restriction mapping

The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein p-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognizes sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs.

Two aspects of the Bennett model are of interest from a mathematical point of view. First there is the question whether Bennett's "ranking method" for predicting the order of chromosomes will always work. The answer depends on the number n of chromosomes: If n is odd, predictions (being not necessarily unique) are possible in most cases. Secondly there is Bennett's procedure for determining the arrangement of chromosomes. It is shown that the method of minimising the perimeter of the polygon obtained by connecting the centromeres is only applicable if the positions of the n centromeres do not deviate too much from an arrangement along a regular n-gon.

Two aspects of the Bennett model are of interest from a mathematical point of view. First there is the question whether Bennett's "ranking method" for predicting the order of chromosomes will always work. The answer depends on the number n of chromosomes: If n is odd, predictions (being not necessarily unique) are possible in most cases. Secondly there is Bennett's procedure for determining the arrangement of chromosomes. It is shown that the method of minimising the perimeter of the polygon obtained by connecting the centromeres is only applicable if the positions of the n centromeres do not deviate too much from an arrangement along a regular n-gon.

comprise the specialized structure of the synaptic junc-Neuroendocrine-Dlg (NE-Dlg) is a member of the tion (15). Their role in nonneural tissues is less clear, discs-large-related (DLG) subfamily of the membranebut it seems likely that they also function in the assemassociated guanylate kinase-related protein family. bly of cell junctions in these tissues (9, 17).

Strategies to construct the physical map of the Trypanosoma cruzi nuclear genome have to capitalize on three main advantages of the parasite genome, namely (a) its small size, (b) the fact that all chromosomes can be defined, and many of them can be isolated by pulse field gel electrophoresis, and (c) the fact that simple Southern blots of electrophoretic karyotypes can be used to map sequence tagged sites and expressed sequence tags to chromosomal bands. A major drawback to cope with is the complexity of T. cruzi genetics, that hinders the construction of a comprehensive genetic map. As a first step towards physical mapping, we report the construction and partial characterization of a T. cruzi CL-Brener genomic library in yeast artificial chromosomes (YACs) that consists of 2,770 individual YACs with a mean insert size of 365 kb encompassing around 10 genomic equivalents. Two libraries in bacterial artificial chromosomes (BACs) have been constructed, BACI and BACII. Both libraries represent about three genome equivalents. A third BAC library (BAC III) is being constructed. YACs and BACs are invaluable tools for physical mapping. More generally, they have to be considered as a common resource for research in Chagas disease.

As part of the Trypanosoma cruzi Genome Initiative, we have mapped a large portion of the chromosomal bands XVI (2.3 Mb) and XVII (2.6 Mb) containing the highly repetitive and immunodominant antigenic gene families h49 and jl8. Restriction mapping of the isolated chromosomal bands and hybridization with chromosome specific gene probes showed that genes h49 and jl8 are located in a pair of size-polymorphic homologous chromosomes. To construct the integrated map of the chromosomes harboring the h49 andjl8 loci, we used YAC, cosmid, and λ phage overlapping clones, and long range restriction analysis using a variety of probes (i.e., known gene sequences, ESTs, polymorphic repetitive sequences, anonymous sequences, STSs generated from the YAC ends). The total length covered by the YAC contig was approximately 670 kb, and its map agreed and was complementary to the one obtained by long-range restriction fragment analysis. Average genetic marker spacing in a 105 kb region around h49 and jl...

Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for finescale mapping and gene finding and as initial steps for either a high-or a low-redundancy sequencing effort. Such strategies are highly automatable.

Plasmid pEST4011 enables Pseudomonas putida Paw85 to degrade 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoate (3-CBA). This new 2,4-D degradative plasmid has considerable homology with the regions of pJP4 containing the 2,4-D degradative genes (tfd). Restriction fragment BamHI-B of plasmid pEST4011, which has homology with this region, was cloned into the broad-host-range vector pKT240 and studied in P. putida PaW85. Restriction mapping, hybridization analysis and enzyme assays established the location of the genes for 2,4-D monooxygenase (tfdA), 2,4-dichlorophenol hydroxylase (tfdB), chlorocatechol 1,2-dioxygenase (tfdC) and the tfdR and tfdS regulatory genes on this fragment. Plasmid pEST4012 is a derivative of pEST4011 derived through the spontaneous deletion of a 42 kbp DNA fragment, which results in the loss of the 2,4-D+ and 3-CBA+ phenotype. We present here the physical maps of pEST4011 and pEST4012. In spite of the similarities in functions, the size (70 kbp), order of catabolic genes and restriction pattern of pEST4011 are clearly different from those of pJP4.

An interval containment model of a graph maps vertices into intervals of a line in such a way that two vertices are adjacent if and only if the corresponding intervals are comparable under the inclusion relation. Graphs admitting an interval containment model are called containment interval graphs or CI graphs for short. A vertex v of a CI graph G is an end-vertex if there is an interval containment model of G in which the left endpoint of the interval corresponding to v is less than all other endpoints. In this work, we present a characterization of end-vertices in terms of forbidden induced subgraphs.

Many problems involving DNA can be modeled by families of intervals. However, traditional interval graphs do not take into account the repeat structure of a DNA molecule. In the simplest case, one repeat with two copies, the underlying line can be seen as folded into a loop. We propose a new definition that respects repeats and define loop graphs as the intersection graphs of arcs of a loop. The class of loop graphs contains the class of interval graphs and the class of circular-arc graphs. Every loop graph has interval number 2. We characterize the trees that are loop graphs. The characterization yields a polynomial-time algorithm which given a tree decides whether it is a loop graph and, in the affirmative case, produces a loop representation for the tree.

A refined physical map of chromosome 17q21.31 uncovered a 900-kb inversion polymorphism. Chromosomes with the inverted segment in different orientations represent two distinct lineages, H1 and H2, that have diverged for as much as 3 million years and show no evidence of having recombined. The H2 lineage is rare in Africans, almost absent in East Asians but found at a frequency of 20% in Europeans, in whom the haplotype structure is indicative of a history of positive selection. Here we show that the H2 lineage is undergoing positive selection in the Icelandic population, such that carrier females have more children and have higher recombination rates than noncarriers.

Nectria haematococca mating population I (MPI, anamorph, Fusarium solani f. sp. cucurbitae race 1) is the causal agent of Fusarium crown and foot rot disease of cucurbits. It occurs worldwide, causing serious damages on the cucurbits cultivations. Although genetic studies on this fungus were ahead of genetic analysis of other plant pathogenic fungi in early 1940s, such investigations ceased after 1970. For performing genetic analysis, irrespective of whether it is conventional or molecular, and also in pursuing whole genome sequencing, information of karyotype is the underlying basis. As to the karyotype of N. haematococca MPI, cytological investigations were done more than 50 years ago, in which haploid chromosome number (CN) of this fungus was estimated to be n=4, Thereafter, no additional data have been added to the cytological karyotype of this fungus. In this study, I present a reliable karyotype of this important plant pathogen, N. haematococca MPI using two standard strains ATCC18098 and ATCC18099, by combining molecular and cytological karyotyping methods. In addition, a mini-chromosome discovered during the course of karyotyping was analyzed for its cytological nature and meiotic inheritance mode. Molecular karyotyping using pulsed field gel electrophoresis (PFGE) of ATCC18098 and ATCC18099 was attempted using a standard running condition of PFGE suitable to separate chromosomes below ~ 6 Mb. Results showed apparent similarity in the banding pattern of the two strains and two middlesized chromosome bands were clearly resolved. The two bands migrated similarly between the two strains and their sizes were estimated to be ~ 3.5 and ~ 2.5 Mb. Besides these bands, an extra small band was detected in ATCC18098 with a size of ca. 410 kb. Southern hybridization of this band with telomere repeats (TTAGGG)n from Neurospora crassa as a probe showed the presence of telemetric repeats within this band suggesting that this band is a miniv In the name of Allah Most Gracious Most Merciful. All praise and thanks to Allah the exalted, the Lord of the universe, May the choicest blessings and peace of Allah be upon the last Messenger and Prophets, Muhammad, his family, Companions and all those who follow his footsteps. I am very grateful to Associate Prof. Dr. Masatoki Taga for suggesting the point, his precise instructions through the study, for many helpful discussions, for critical reading the manuscript, for his patience and kindheartedness and for his unlimited and unconditional support during the past years. I appreciate Prof. Kamada for his support and fruitful discussions, Prof. Takahashi Taku for his supervision and Dr. Muraguchi (Akita Prefectural University) for providing the Operon RAPD primers. I also appreciate to all former and current members of Dr. Taga' lab: Nishima, Tsuchiya, Kaneko, Songlin, Arimoto, Ogura, Nishizawa and my brother Hamid for their encouragement, support, and fun time together. Last but not least, I want to thank my dear wife and children for unconditional love and infinite patience, my family and my family-in-law for encouragement and support, the Egyptian group in Okayama for their endless support and to all the members of Okayama muslim community.

We have developed a new technique for the generation of YAC contigs in the mouse genome that is based on the ability to detect overlapping clones by hybridization of shared IRS-PCR products. As a demonstration of the technique, a 5-cM, >5 megabase contig was developed on the distal half of mouse Chromosome (Chr) 1, spanning the region from Lamb2 to At3. The contig covers roughly 5% of the genetic distance of the chromosome and is comprised of more than 80 clones; 71 probes were assigned physical order on the chromosome, of which 59 were new markers generated in this study. Eight of the new probes were shown to be polymorphic between C3H/HeJgld and M. spretus. Three probes were mapped on a [(C3H/HeJ-gld • M. spretus) • C3H/HeJ-gld] interspecific backcross to integrate the physical map with a highresolution genetic map of the region.

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1s on each row are consecutive. These matrices are used for DNA physical mapping and ancestral genome reconstruction in computational biology on the other hand they represents a class of convex bipartite graphs and are of interest of algorithm graph theory researchers. Tucker gave a forbidden submartices characterization of matrices that have C1P property in 1972. Booth and Lucker (1976) gave a first linear time recognition algorithm for matrices with C1P property and then in 2002, Habib, et al. gave a simpler linear time recognition algorithm. There has been substantial amount of works on efficiently finding minimum size forbidden submatrix. Our algorithm is at least n times faster than the existing algorithm where n is the number of columns of the input matrix.