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PubMed1977

Correlations between chromosome segments and fitness in Drosophila melanogaster. I. The X chromosome and egg production.

Unmarked segments within the X chromosomes of four different Drosophila melanogaster isogenic lines were assessed with respect to egg production. By making a series of crosses among original and derived recombinant lines, it was possible to estimate parameters representing additive, dominance and interaction effects of the segments. It was shown that whereas most of the segments were additive for egg production when homozygous, they all displayed dominance in the heterozygous condition. Two of the strains were characterized by intersegmental interaction. A possible position effect was detected for these same two strains, with flies in the coupling phase laying more eggs than those in the repulsion configuration. There was no apparent relationship between the number of eggs laid and the amount of heterozygosity within the X chromosome.

Animals↗
PubMed1991

Directed synthesis of a segmental chromosomal transposition: an approach to the study of chromosomes lethal to the gametophyte generation of maize.

Because of the haploid nature of the gametophyte generation of plants, most mutations that are lethal or detrimental to the gametophytes cannot be recovered. Our laboratory is currently developing several techniques to overcome this situation. In this paper, a procedure is described to generate directed segmental chromosomal transpositions. The method involves recovery of recombinants between reciprocal translocation overlaps such that one region of the genome is inserted into a nonhomologous chromosome in a predetermined and directed manner. This duplicated segment then could serve to cover deficiencies or mutations, lethal to the gametophytes, in the region from whence it originated. The manipulation of segmental chromosomal transpositions for analyzing mutants lethal or detrimental to the gametophyte generation is discussed. The procedure to generate transpositions, the translocations between normal A and supernumerary B chromosomes that generate deficiencies in the male gametes, the r-X1 chromosome that generates deficiencies in the female gametes and other techniques available in maize form a system to analyze gametophyte lethal mutations.

Alcohol Dehydrogenase↗
PubMed1978

A long unidentifiable extra chromosomal segment--a possible duplication of human 7q.

Limitation of current techniques in identifying extra chromosomal segments arising de novo is illustrated by a putative case of a duplication of the long arm of chromosome 7. The propositus, demonstrating multiple congenital anomalies and severe mental retardation, had a large extra segment of chromatin on chromosome 7q that was absent in his parents. The banding pattern of this segment resembled that of the long arm of chromosomes 7, 8, or 9. Various procedures indicated that the additional material did not include the secondary constriction of 9q. The phenotype of the propositus did not fit well with that of trisomy 8.

Abnormalities, Multiple↗
PubMed2001

Escape from repeat-induced point mutation of a gene-sized duplication in Neurospora crassa crosses that are heterozygous for a larger chromosome segment duplication.

In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced point mutation (RIP) in its target gene was suppressed in crosses that were heterozygous for another larger chromosome segment duplication. Specifically, the frequency of RIP in the erg-3 gene due to a 1.3-kb duplication was reduced if the chromosome segment duplications Dp(IIIR > [I;II]) AR17, Dp(VIR > IIIR) OY329, or Dp(IVR > VII) S1229 were present in either the same or the other parental nucleus of the premeiotic dikaryon. We suggest that the larger duplications act as sinks to titrate the RIP machinery away from the smaller duplication. In contrast, RIP efficiency was relatively unaffected in comparably unproductive interspecies crosses with N. intermedia and N. tetrasperma. These findings offer a novel explanation for the observed persistence of the transposable element Tad in only a subset of Neurospora strains.

Chromosomes, Fungal↗
PubMed1984

Spontaneous duplications and transpositions of a large chromosome segment in Aspergillus nidulans.

Spontaneous revertants of the leaky adE20 mutant of Aspergillus nidulans were obtained as vigorous sectors emerging from stunted colonies on adenine-free medium. Among the genetically heterogeneous sectors up to about 20% were recognized unequivocally as having an additional chromosome segment bearing adE20; two doses of this leaky allele permitted growth without added adenine. Eleven spontaneous duplication strains of independent origin were analysed genetically. Eight carried the duplicate segment on chromosome IIR; three of these, phenotypically similar to all eight, were analysed in detail and were shown-within the limits of such genetic analysis - to have a large, terminal segment of IR duplicated and attached terminally and uninverted to IIR. One strain had a duplication, possibly tandem, on IR and two had duplications attached elsewhere in the genome. The results suggested a preferential site for the initiation of duplicate segments in this system, as well as a preferential site for their attachment. Agents known to modify instability of a previously studied Dp(IR----IIR) strain affected the frequency of duplications among selected adE20 revertant sectors and/or the genomic locations of duplicated segments. Trypan blue and coumarin, which enhance Dp(IR----IIR) instability in a specific way, and Co2+, which stabilizes Dp(IR----IIR), gave 14, 50 and 62% duplication sectors respectively, among revertants. Duplications selected in the presence of Co2+ had mainly IIR attachments; of those from trypan blue and coumarin, about one-quarter were attached to IIL and none to IIR.

Aspergillus nidulans↗
PubMed2003

Mapping QTL for traits associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using japonica chromosome segment substitution lines.

A mapping population of 66 japonica chromosome segment substitution lines (CSSLs) in indica genetic background, derived from a cross between a japonica variety Asominori and an indica variety IR24 by the single-seed descent, backcrossing and marker-assisted selection, was used to detect quantitative trait loci (QTLs) for leaf bronzing index (LBI), stem dry weight (SDW), plant height (PH), root length (RL) and root dry weight (RDW) under Fe2+ stress condition in rice. Two parents and 66 japonica CSSLs were phenotyped for the traits by growing them in Fe2+ toxicity nutrient solution. A total of fourteen QTLs were detected on chromosome 3, 6, 7, 9, 11 and 12, respectively, with LOD of QTLs ranging from 2.72 to 6.63. Three QTLs controlling LBI were located at the region of C515-XNpb279, R2638-C1263 and G1465-C950 on chromosome 3, 9 and 11, their contributions to whole variation were 16.45%, 11.16% and 28.02%, respectively. Comparing with the other mapping results, the QTL for LBI located at the region of C515-XNpb279 on chromosome 3 was identical with the QTL for chlorophyll content on a rice function map. The results indicated that ferrous iron toxicity of rice is characterized by bronzing spots on the lower leaves, which spread over the whole leaves, causing the lower leaves to turn dark gray and to product chlorophyll catabolites or derivatives which reduce cytotoxicity of some heavy metals, such as ferrous iron. Furthermore, the QTL for LBI, SDW and RDW located at the region of G1465-C950 on chromosome 11 is a major QTL. Whether the QTL for SDW, PH, RL and RDW at the region of XNpb386-XNpb342 on chromosome 6 is associated with resistance to ferrous iron toxicity need further studies. Our goal is to identify breeding materials for resistance to Fe2+ toxicity through marker-assisted selection based on the detected markers.

Chromosome Mapping↗
PubMed2002

Transmission disequilibrium test for hand bone mineral density and 11q12-13 chromosomal segment.

The main aim of the present study was to test the hypothesis that the bone mineral density (BMD) assessed from radiographs of the hand phalanges in a random sample of ethnically homogeneous pedigrees is linked to the 11q12-13 chromosomal segment. The data for the study were gathered from 574 Chuvasha individuals belonging to two- and three-generation pedigrees who live in small villages in the Bashkortostan autonomy, Russia. Preliminary statistical-genetic analysis of the BMD in the pedigrees studied showed that potential genetic effects were highly significant ( p<0.001, in comparison with the model assuming no genetic effect), and explained at least 36% of the BMD variation adjusted for sex and age differences. For the transmission/disequilibrium test (TDT) used in our study, a total of 163 nuclear families with two sibs on average were available. Seven DNA microsatellite markers ( D11S1313, D11S1765, D11S987, D11S913, D11S983, D11S1314, D11S916) with average spacing of 2 cM on the chromosomal area 11q12-13 were selected for the TDT. The nominal p values ( p<0.05-0.0015) obtained from three TDT-type tests used for random and extreme-threshold sampling designs pointed consistently to possible linkage disequilibrium between BMD and some of the DNA markers. There was evidence for possible linkage disequilibrium in the upper part of the chromosomal segment studied (markers D11S1313 and D11S1765), and also in the lower part (markers D11S1983 and D11S1314). The lowest nominal p values (0.0015-0.0067) were obtained from three TDT-type tests for marker D11S1313. However, our findings must still be treated with great caution.

Adult↗
PubMed2002

Prognostic significance of molecular genetic aberrations on chromosome segment 11p15.5 in non-small-cell lung cancer.

PURPOSE: The assessment of prognosis and decisions on treatment for patients with non-small-cell lung cancer (NSCLC) are determined on the basis of disease stage and performance status. NSCLC frequently manifests loss of heterozygosity (LOH) at chromosome segment 11p15.5. Whether LOH at 11p15.5 is an independent prognostic variable has yet to be determined. PATIENTS AND METHODS: We developed five novel markers, which can be assessed by polymerase chain reaction and restriction enzyme digestion. LOH at 11p15.5 was assessed in 193 patients who underwent surgical resection for pathologic stage I and II of the disease. RESULTS: LOH at 11p15.5 was associated with poor survival (P =.021). Multivariate logistic regression analysis showed that after disease stage, performance status, weight loss, sex, age at diagnosis, and smoking history were controlled for, patients with LOH were two times more likely to die than those without LOH (relative risk [RR] = 2.01, P =.021). Cox regression analysis with disease stage and LOH revealed that the survival of patients with stage I disease and LOH was similar to the survival of patients with stage II disease, and it was significantly worse than the survival of stage I patients without LOH (RR = 2.38, P =.038). CONCLUSION: LOH in a 310-kb region on chromosome segment 11p15.5 that includes the gene for the regulatory subunit of the enzyme ribonucleotide reductase is highly predictive of poor survival from NSCLC. The future utility of analysis of the allelic status of this region may involve treatment decisions, such as the use of neoadjuvant and adjuvant chemotherapy for patients with stage I disease.

Carcinoma, Non-Small-Cell Lung↗
PubMed2001

Conserved vertebrate chromosome segments in the large salamander genome.

Urodele amphibians (salamanders) are important models for embryological, physiological, and natural history research and are also a biomedically important group because they are the only vertebrates capable of regenerating entire organ systems. To enhance the utility of salamanders for biomedical research and for understanding genome evolution, genetic linkage analysis was used to identify chromosome segments that are homologous between ambystomatid salamanders and distantly related vertebrate model organisms. A total of 347 loci (AFLPs, RAPDs, and protein-coding loci) were mapped using an interspecific meiotic mapping panel (Ambystoma mexicanum and A. tigrinum tigrinum; family Ambystomatidae). Genome size in Ambystoma was estimated to be 7291 cM, the largest linkage map estimate reported for any organism. However, the relatively large size of the salamander genome did not hinder efforts to map and identify conserved syntenies from a small sample of 24 protein-coding loci. Chromosomal segments that are conserved between fishes and mammals are also conserved in these salamanders. Thus, comparative gene mapping appears to be an efficient strategy for identifying orthologous loci between ambystomatid salamanders and genomically well-characterized vertebrate model organisms.

Animals↗
PubMed1992

The theoretical distribution of lengths of intact chromosome segments around a locus held heterozygous with backcrossing in a diploid species.

When two different isogenic lines of a diploid species (or two different species) are crossed, the resulting F1 individuals should be heterozygous at all the loci fixed for different alleles in the two strains (in the limit, at all the loci of the genome). If one of these loci is then held heterozygous for several generations of repeated backcrossing to the same strain, the average length of intact chromosome segments (with reference to the original parental chromosome) on both sides of the selected locus, or, equivalently, the average length of segments surrounding that locus which are still heterozygous (with reference to the fully heterozygous F1 chromosome), may diminish, but cannot increase. Several authors have derived equations to predict this average. We show that the most widely used criterion, developed by R.A. Fisher, leads to serious overestimations of the true parametric values, when applied to early generation analyses, with the corresponding errors in the interpretation of experimental results. We then derive the exact equations both for the average and standard deviation of the lengths of intact chromosome segments surrounding a locus held heterozygous after any number of generations of backcrossing. Our results are in close agreement with those found by a former author, although involving a rather different approach.

Alleles↗
PubMed2006

[Transfer of a rye small chromosomal segment with powdery mildew-resistant gene(s) into common wheat (Triticum aestivum L.)].

The advanced progeny lines (BC1F5) from the monosomic addition lines between common wheat cultivar Mianyang 11, which is highly susceptible to powdery mildew, and an inbred rye line R12 were analyzed for selection of wheat-rye translocations. Based on a rye-specific repetitive sequence of pSc20H, which spread over all chromosomes of rye but did not existed in wheat, a set of PCR primer was designed and used to identify the rye chromosome segments in wheat. From 300 of the BC1F5 progeny lines 70 were found to contain chromosome composition of rye. An advanced line, 96II691-830-98, originated from 6R monosomic addition line was observed to be immune to powdery mildew, different from its wheat parent Mianyang 11. A small segment of rye chromosome at telomere in a pair of wheat chromosome in the line was found by means of GISH. The results indicated that a small segment of rye chromosome 6R carrying the gene(s) for resistance to powdery mildew has been transferred into common wheat. In the progeny of monosomic addition lines a high frequency of wheat-alien species translocation with various segments of chromosomes could be found by application of both PCR and GISH technique.

Chromatin↗
PubMed1993

Aberrations of chromosome segment 12q13-15 characterize a subgroup of hemangiopericytomas.

BACKGROUND: In later years, several characteristic acquired chromosomal aberrations have been identified in mesenchymal tumors. Many of these aberrations, either alone or with histopathologic and clinical data, are useful in diagnosis. The cytogenetic profile of hemangiopericytomas has been poorly investigated. METHODS: Short-term cultures from four spindle cell tumors were cytogenetically analyzed. RESULTS: Clonal acquired chromosome aberrations were found in three of the four tumors: inv(12) (q14q24) in a malignant hemangiopericytoma, a supernumerary der(3)t(3;12) (p21-23;q13-15) in a benign hemangiopericytoma, and t(6;12;19) (p21;q13;p13) in a spindle cell sarcoma that was histologically a malignant hemangiopericytoma or a synovial sarcoma. The fourth tumor, a malignant hemangiopericytoma, had a normal karyotype. The tumors with inv(12) and t(6;12;19) had subclones with trisomy 5 in addition to the structural changes. CONCLUSIONS: The current findings and the literature data indicate that a subgroup of hemangiopericytomas is characterized by rearrangement of chromosome segment 12q13-15.

Adult↗
PubMed1999

A 1.4-Mb high-resolution physical map and contig of chromosome segment 11p15.5 and genes in the LOH11A metastasis suppressor region.

The centromeric part of chromosome segment 11p15.5 contains a region of frequent allele loss in many adult solid malignancies. This region, called LOH11A, is lost in 75% of lung cancers and is thought to contain a gene that may function as a metastasis suppressor. Genetic complementation studies have shown suppression of the malignant phenotype including reduction of metastasis formation. We constructed a high-resolution physical map and contig over 1.4 Mb that includes the beta-hemoglobin gene cluster and the gene for the large subunit of ribonucleotide reductase (RRM1). Through sequencing and computerized analysis, we determined that this region contains an unusually large number of transposable elements, which suggests that double-stranded DNA breaks occur frequently here. Twenty-two putative genes were identified. Because of its location at the site of maximal allele loss in the 650-kb LOH11A region and previous functional studies, RRM1 is the most likely candidate gene with metastasis suppressor function. The malignant phenotype, in this case, results from a relative loss of function rather than a complete loss.

Adenocarcinoma↗
PubMed1982

In vitro replication of recombinant plasmids carrying chromosomal segments of Xenopus laevis.

Recombinant plasmids carrying a segment of Xenopus laevis chromosomal DNA were constructed with plasmid pBR322 as the vector. A recombinant plasmid pXY65 carrying a 3.2-kilobase BamHI segment of the chromosome of X. laevis has been found to contain a repetitive sequence dispersed throughout the X. laevis chromosomes. This plasmid initiated replication in vitro when the supercoiled circular molecules were incubated in a replication system. The other recombinant plasmids tested and the pBR322 vector were not replicated. Electron microscopic analysis of the replicative intermediates showed that the replication was initiated at a specific site in the 3.2-kilobase BamHI segment of pXY65 and that the replication usually proceeded bidirectionally. Analysis of the reaction products by centrifugation in alkaline sucrose gradients indicated that short pieces were synthesized in the in vitro replication system. DNA synthesis was inhibited in vitro by the addition of aphidicolin and by omission of dNTPs. These results indicate that the X. laevis segment cloned in pXY65 contains a site capable of initiating replication in vitro.

Animals↗
PubMed2000

SSA/RO52gene and expressed sequence tags in an 85 kb region of chromosome segment 11p15.5.

Frequent allelic loss in lung cancer has been described in a region on chromosome segment 11p15.5 (LOH11A). The region is approximately 650 kb in size and flanked by the markers D11S988 centromeric and D11S860 telomeric. Clinical and cell biological studies suggest that it contains a gene associated with metastatic tumor spread. One of the genes identified within this region is SSA/Ro52, which has a RING finger domain and may be involved in gene regulation. We studied this gene for mutations using SSCP analysis and for expression using RT-PCR and Western blotting on lung cancer cell lines and tumor-normal tissue pairs. No mutations and no differences in mRNA or protein expression between tumor tissue and normal tissue pairs were identified. We discovered a novel polymorphic site (SSA44C/T) within exon 1 of this gene. Among 141 primary lung cancers, allelic loss was observed in 16% of informative cases. Our analyses excluded SSA/Ro52 as a tumor-suppressor gene in lung cancer and newly defined the centromeric border of the LOH11A region from D11S988 previously to SSA44C/T. This reduced the region of the putative suppressor gene to 460 to 485 kb. A significant difference (p = 0.01) in the frequency of alleles for this polymorphism between Caucasians and African-Americans was observed. The "T" allele frequency was 0.12 in Caucasians and 0.23 in African-Americans. A genomic EcoRI map over 85 kb surrounding the SSA/Ro52 gene was constructed, and 4 expressed sequence tags were identified by sequencing and studied.

Alleles↗
PubMed1986

[Inversion of the metE-oriC-rpsE chromosome segment in Escherichia coli K12].

We have described recently a large inversion of the Escherichia coli chromosome (designated udpPf1), including region of the chromosomal replication region (oriC). The udpPf1 inversion was induced by Tn10 transposon (metE::Tn10). It results in increased expression of the uridine phosphorylase gene (udp) which is closely linked to the metE gene. The data of conjugational and transductional experiments presented in this report demonstrate that the udpPf1 inversion covers a chromosomal segment extending over 12 min of the E. coli genetic map and including the rpsE, crp and metE::Tn5 markers. The results are presented indicating that the increased uridine phosphorylase activity is due to fusion of the udp gene to a more strong promoter located, probably, in the operon for ribosomal proteins cluster, near 73 min on the E. coli chromosome.

Chromosome Inversion↗
PubMed2001

Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer.

Molecular, functional, and clinical analyses strongly suggest that chromosome segment 11p15.5 contains a gene involved in lung cancer pathogenesis. The critical region of allele loss is 310 kb in size. We used our contig of P1-phage artificial chromosome (PAC) clones together with newly identified bacterial artificial chromosome (BAC) clones and the draft human genome sequence to complete a contiguous string of 380 407 bp. Three PAC clones that span the region were used to identify transcripts by exon trapping. Computational gene prediction algorithms were used to query the sequence for potential genes and exons. Screening for expression was performed with tissue-specific and cell line derived mRNA arrays. The region contains the complete SSA/Ro52 and RRM1 genes, exons 7-12 of the GOK gene, and the psirad pseudo-gene. A cluster of six nearly identical genes with an intact open reading frame (ORF) of 585 bp that share 75% identity with the HSPC182 gene was found. In addition, five putative novel genes were identified. Sequence tagged sites (STS) and polymorphic markers were used to screen 117 lung cancer cell lines for homozygous deletions and none were identified. These data provide the basis for the identification of a lung cancer suppressor gene on 11p15.5.

Base Sequence↗