Two-dimensional screening of the Wageningen chicken BAC library

We have constructed a Bacterial Artificial Chromosome (BAC) library that provides 5.5-fold redundant coverage of the chicken genome. The library was made by cloning partial HindIII-digested high-molecular-weight (HMW) DNA of a female White Leghorn chicken into the HindIII site of the vector pECBAC1. Several modifications of standard protocols were necessary to clone efficiently large partial HindIII DNA fragments. The library consists of 49,920 clones arranged in 130 384-well plates. An average insert size of 134 kb was estimated from the analysis of 152 randomly selected BAC clones. The average number of NotI restriction sites per clone was 0.77. After individual growth, DNA was isolated of the pooled clones of each 384-well plate, and subsequently DNA of each plate was isolated from the individual row and column pools. Screening of the Wageningen chicken BAC library was performed by two-dimensional PCR with 125 microsatellite markers. For 124 markers at least one BAC clone was obtained. FISH experiments of 108 BAC clones revealed chimerism in less than 1%. The number of different BAC clones per marker present in the BAC library was examined for 35 markers which resulted in a total of 167 different BAC clones. Per marker the number of BAC clones varied from 1 to 11, with an average of 4.77. The chicken BAC library constitutes an invaluable tool for positional cloning and for comparative mapping studies.

A comprehensive microsatellite linkage map of the chicken genome

A comprehensive linkage map of the chicken genome has been developed by segregation analysis of 430 microsatellite markers within a cross between two extreme broiler lines. The population used to construct the linkage map consists of 10 families with a total of 458 F2 individuals. The number of informative meioses per marker varied from 100 to 900 with an average of 400. The markers were placed into 27 autosomal linkage groups and a Z-chromosome-specific linkage group. In addition, 6 markers were unlinked, 1 of which was Z chromosome specific. The coverage within linkage groups is 3062 cM. Although, as in other species, the genetic map of the heterogametic sex (female) is shorter than the genetic map of the homogametic sex (male), the overall difference in length is small (1.15%). Forty-five of the markers represent identified genes or ESTs. Database homology searches with the anonymous markers resulted in the identification of a further 9 genes, bringing the total number of genes/ESTs on the current map to 54. The mapping of these genes led to the identification of two new regions of conserved synteny between human and chicken and confirmed other previously identified regions of conserved synteny between human and chicken. The linkage map has 210 markers in common with the linkage maps based on the East Lansing and Compton reference populations, and most of the corresponding linkage groups in the different maps can be readily aligned.

Effectiveness in inhibition of recovery of cell survival by cisplatin and carboplatin: influence of treatment sequence

Clinical protocols have been designed to combine platinum-based drugs and radiation in the treatment of cancer. The rationale for this approach has been developed from preclinical studies demonstrating that platinum compounds can potentiate the cytotoxic effects of radiation toward cells. In the present study multicellular spheroids derived from squamous cell carcinoma cell line HN-1 have been used to study the effects of both cisplatin and carboplatin when administered prior to, concurrently, and after irradiation treatment. To study the influence of platinum compounds on sublethal damage repair, single and split doses of radiation were applied. Growth delay and proportion cured spheroids served as endpoints. Both cisplatin and carboplatin had no potentiating effect when administered 24 hr prior to irradiation. When administered 3 hr after completion of irradiation procedures, growth delay after single and split doses were enhanced to the same extent. The drug enhancement ratio for cisplatin was larger (1.5) than for carboplatin (1.2). Both single and split doses were enhanced by the same factor, which was interpreted as no effect on sublethal damage repair. When platinum compounds were present in the target cells at the time of irradiation, especially the split dose radiation response was strongly enhanced: the drug enhancement ratio was 3.9 for cisplatin and 3.2 for carboplatin. Recovery from sublethal damage was totally repressed. This study shows that platinum compounds can potentiate radiation and that for maximum effect the sequence of the two treatment modalities is of utmost importance. Moreover, these results may in part explain the heterogeneous outcomes of trials combining platinum compounds and radiation.

Preliminary linkage map of the chicken (Gallus domesticus) genome based on microsatellite markers: 77 new markers mapped

Microsatellite polymorphisms are finding increasing use in genetics. The objectives of this study were 1) to enlarge the number of markers to contribute to a well-defined linkage map of the chicken genome; and 2) to create a preliminary linkage map only based on microsatellite markers. The need for microsatellite markers is high for performing a whole genome scan for the identification of quantitative trait loci. Seventy-seven newly developed microsatellite markers that were polymorphic on either one or both of the reference populations were mapped and in combination with all previously described markers, used to construct a preliminary linkage map of the chicken genome. The 128 microsatellite markers mapped thus far cover 23 of the 38 linkage groups of the East Lansing reference population. In the case of the Compton reference population, 20 linkage groups out of 40 are covered with microsatellite markers. No linkage was found in the East Lansing population with five markers, and in the case of the Compton population four markers were unlinked. About 42 and 32% of the East Lansing and Compton maps, respectively, were covered by the 128 microsatellite markers. The microsatellite markers are well dispersed among the various linkage groups and there was no evidence for clustering of the markers within the map. With the 38 markers that were mapped on both reference populations, 10 of the East Lansing linkage groups could be associated with 13 of the Compton linkage groups.

New microsatellite markers in chicken optimized for automated fluorescent genotyping

We have isolated and developed 180 new polymorphic chicken microsatellite markers. In addition, primers have been developed for 91 microsatellites derived from the GenBank sequence database (isolated by the laboratory of Terry Burke, Leicester University), of which 89 were polymorphic, and six existing polymorphic markers (HUJ) have been modified. The primer sequences were designed to allow optimal performance of the markers, in sets containing multiple microsatellites, on ABI sequencers. The average number of alleles for the 275 polymorphic markers described was 4.0. Of these markers, 93% were polymorphic in the Wageningen resource population whereas 57% of the markers were polymorphic in the East Lansing reference population and only 44% could be mapped in the Compton reference population. The microsatellite markers described in this paper, in combination with the microsatellite markers published previously, are particularly well suited for performing a total genome scan for the detection of quantitative trait loci (QTL).

Microsatellite polymorphism in commercial broiler and layer lines estimated using pooled blood samples

For 17 microsatellite markers, allele frequencies were determined in nine highly selected commercial broiler and six highly selected commercial layer lines using pooled blood samples from 60 animals. The average number of marker alleles was 5.8 over all lines, 5.2 over broiler lines, and 3.0 over layer lines. The average number of marker alleles within a line was 2.9, 3.6, and 2.0 for all, broiler, and layer lines, respectively. Over all 15 lines, the average percentage of heterozygosity was 42, whereas the heterozygosity in the broiler lines was 53% and in the layer lines only 27%. In broiler lines, 50% of the marker-line combinations showed a heterozygosity above 60%, whereas this was only 5% in layer lines. Estimation of allele frequencies with microsatellite markers was first assessed in pooled and individual samples before usage in the commercial lines. Allele frequencies for 19 microsatellite markers were estimated in chicken pooled blood samples and compared with allele frequencies from individual typed animals. Similar results were obtained when pooled blood samples (heterozygosity of 35.3%) or individual typed animals (heterozygosity of 34.2%) were used. The method to determine allele frequencies using pooled blood samples is faster, cheaper, and as reliable and repeatable as determining allele frequencies using individual typings.

The gene orders on human chromosome 15 and chicken chromosome 10 reveal multiple inter- and intrachromosomal rearrangements

Comparative mapping between the human and chicken genomes has revealed a striking conservation of synteny between the genomes of these two species, but the results have been based on low-resolution comparative maps. To address this conserved synteny in much more detail, a high-resolution human-chicken comparative map was constructed from human chromosome 15. Mapping, sequencing, and ordering of specific chicken bacterial artificial chromosomes has improved the comparative map of chromosome 15 (Hsa15) and the homologous regions in chicken with almost 100 new genes and/or expressed sequence tags. A comparison of Hsa15 with chicken identified seven conserved chromosomal segments between the two species. In chicken, these were on chromosome 1 (Gga1; two segments), Gga5 (two segments), and Gga10 (three segments). Although four conserved segments were also observed between Hsa15 and mouse, only one of the underlying rearrangement breakpoints was located at the same position as in chicken, indicating that the rearrangements generating the other three breakpoints occurred after the divergence of the rodent and the primate lineages. A high-resolution comparison of Gga10 with Hsa15 identified 19 conserved blocks, indicating the presence of at least 16 intrachromosomal rearrangement breakpoints in the bird lineage after the separation of birds and mammals. These results improve our knowledge of the evolution and dynamics of the vertebrate genomes and will aid in the clarification of the mechanisms that underlie the differentiation between the vertebrate species.

Multicolour fluorescent detection and mapping of AFLP markers in chicken (Gallus domesticus)

We describe the mapping of amplified restriction fragment polymorphism (AFLP) markers in chicken (Gallus domesticus) using a multi-colour fluorescent detection system. DNA was used from a population consisting of four families with a total of 183 F2 individuals. The enzyme combination EcoRI/TaqI was used for double digestion, and fluorescently labelled fragments were analysed on an ABI PRISM 377 DNA sequencer. Polymorphic signals in the range of 50-500 bp were genotyped with the ABI PRISM Genotyper 2.0 software, which enabled the analysis of both dominant and incomplete dominant markers (with respect to AFLP, often referred to as codominant). In 19 sets consisting of 3 EcoRI/TaqI primer pair combinations each, a total of 475 polymorphic markers was detected. From these polymorphisms 344 markers could be mapped on the Wageningen linkage map. Fourteen markers were length polymorphisms of the same fragment and 28 markers Z-linked and uniformative; 64 AFLP markers appeared to be unlinked and 25 AFLP markers could not be accurately mapped on the basis of the genotyping results. The resulting AFLP/microsatellite linkage map is comprised of 33 linkage groups with a total of 835 loci.

Functional genes mapped on the chicken genome

Microsatellite polymorphisms are finding increasing use in genetics. In addition to the random isolation of microsatellite markers, such markers can also be developed from sequences already present in public domain databases. An advantage of public domain databases is that these microsatellites are known to be located within or close to identified functional genes. In this study the GenBank and EMBL databases were screened for microsatellite markers and primers were defined for amplification. Subsequently, these markers were tested on a panel of five different birds from layer and broiler stocks and on the international reference families: the East Lansing reference family and the Compton reference family. Of the 33 loci tested, 25 were polymorphic on the test panel and from these 25, 14 were polymorphic in one or both reference families. Twelve of the 14 loci that could be mapped fell into previously defined linkage groups. The other two markers were not linked. Because three of the loci had previously been mapped to specific chromosomes by in situ hybridization, linkage groups E6 and C3 could be assigned to chromosome 6, E5 and C17 to chromosome 4 and E21 to one of the microchromosomes.

Highly polymorphic microsatellite markers in poultry

Microsatellite markers have been established for a large number of species, but up till now very few polymorphic microsatellite markers have been reported in poultry. We have isolated 34 polymorphic chicken microsatellite markers of the poly(TG) type. The number of repeats varied from 9 up to 33. Often, other repeats such as poly(T) or poly (GAA) were present adjacent to the poly (TG) repeat. Polymerase chain reaction amplification of the microsatellites resulted in detection of three or more alleles in a test panel of five different animals for 75% of the microsatellites. Segregation of five microsatellite markers has been tested in a small family.

New microsatellite markers on the linkage map of the chicken genome

Ten polymorphic microsatellite markers mainly of the poly (TG) type were examined on the two international reference families, the East Lansing reference family and the Compton reference family. Three of the markers were polymorphic on the East Lansing family (linkage groups E), three on the Compton family (linkage groups C), and four were polymorphic on both families. The microsatellite markers were well dispersed among the various linkage groups, and there was no evidence for clustering of the markers within the map. Common microsatellite markers were able to associate linkage groups from the two genetic maps. Association of linkage groups E2 with C4, E10 with C13, and E1 with C15 are found. Linkage group E1 is located on chromosome 1, and because of the association between E1 and C15, C15 is therefore assigned to chromosome 1. A newly defined linkage group (E20) was found in case of microsatellite marker MCW14. The relative distances between markers and the gene order of the markers can change upon addition of more markers to the linkage maps.

Radiosensitivity of different human tumor cells lines grown as multicellular spheroids determined from growth curves and survival data

Five human tumor cell lines were grown as multicellular tumor spheroids (MTS) to determine whether multicellular tumor spheroids derived from different types of tumors would show tumor-type dependent differences in response to single-dose irradiation, and whether these differences paralleled clinical behavior. Multicellular tumor spheroids of two neuroblastoma, one lung adenocarcinoma, one melanoma, and a squamous cell carcinoma of the oral tongue, were studied in terms of growth delay, calculated cell survival, and spheroid control dose50 (SCD50). Growth delay and cell survival analysis for the tumor cell lines showed sensitivities that correlated well with clinical behavior of the tumor types of origin. Similar to other studies on melanoma multicellular tumor spheroids our spheroid control dose50 results for the melanoma cell line deviated from the general pattern of sensitivity. This might be due to the location of surviving cells, which prohibits proliferation of surviving cells and hence growth of melanoma multicellular tumor spheroids. This study demonstrates that radiosensitivity of human tumor cell lines can be evaluated in terms of growth delay, calculated cell survival, and spheroid control dose50 when grown as multicellular tumor spheroids. The sensitivity established from these evaluations parallels clinical behavior, thus offering a unique tool for the in vitro analysis of human tumor radiosensitivity.

Developing microsatellite markers from cDNA: a tool for adding expressed sequence tags to the genetic linkage map of the chicken

A chicken embryonic cDNA library was screened with a (TG)13 probe in order to develop polymorphic microsatellite markers. The redundancy of the embryonic cDNA library with a chicken brain cDNA library, which was used for microsatellite development in a previous study, was extremely high. Of the 300 (TG)13 positive clones, only 80 were unique for the embryonic cDNA library. Still, nine expressed sequences derived from the embryonic cDNA library were mapped in the Wageningen (WAU) resource population. In addition seven microsatellite markers from the chicken brain cDNA library, which were monomorphic or unlinked in the two international reference families in the previous study, were also mapped in the WAU population. Three of the 16 mapped chicken expressed sequence tags (ESTs) showed relatively high percentages of sequence similarity to sequences found in other species. As two of these genes, RAB6 and ZFX/ZFY, have been mapped in humans, they contribute to the comparative map of the chicken.

Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase-polymerase chain reaction and single strand conformation gel purification method

In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription-polymerase chain reaction (RT-PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo-d(T) reverse-primers and 20-mer arbitrary forward-primers. A purification step by single strand conformation gel electrophoresis was added before sequencing. With a ratio of 112 unique sequences out of 155, we found this method to be highly effective when compared with EST production with randomly selected clones from non-subtracted, non-normalized libraries. A large proportion of the ESTs sequenced correspond to genes involved in transcriptional and post-transcriptional events. Cytogenetic mapping was performed for a subset of ESTs and four regions of conserved synteny between chicken and human were confirmed.

Development and mapping of polymorphic microsatellite markers derived from a chicken brain cDNA library

Until now the genetic linkage map in chicken has ben based mainly on random genomic markers. The addition of expressed sequence tags (ESTs) to the genetic linkage maps is becoming more important because ESTs can form the basis for comparative mapping studies. This may be helpful for the detection of candidate genes for quantitative trait loci (QTLs). In our study we used a (TG)13 repeat as probe for the detection of microsatellites in a chicken brain cDNA library. After hybridization 0.15% of the cDNA clones gave a positive signal. The cDNA complexity of the library was high; of the 90 cDNA clones that were sequenced 60 occurred only once. For 29 clones primer sets for the polymerase chain reaction could be developed. Twenty-one microsatellites were polymorphic on one or more of the test panels and 15 markers could be mapped on either or both of the international reference families. Because sequence homology between chicken and mammalian cDNAs is sometimes low it was difficult to assess the level of sequence homology that indicated a true homologous transcript. In our study seven cDNA cones, of which three could be mapped, showed a relatively high percentage of sequence homology with sequences found in other species. Because sequencing and mapping of expressed sequence tags in human and mouse is progressing very rapidly, it is predicted that further information will soon be readily available. Therefore, increasing the number of expressed sequences on the chicken genetic linkage map will be of value for comparative mapping studies in the near future.

Extending the chicken-human comparative map by placing 15 genes on the chicken linkage map

To increase the number of type I loci on the chicken linkage map, chicken genes containing microsatellite sequences (TAn, CAn, GAn, An) were selected from the nucleotide sequence database and primers were developed to amplify the repeats. Initially, 40 different microsatellites located within genes were tested on a panel of animals from diverse breeds, and identified 17 polymorphic microsatellites. These polymorphisms allowed us to add 15 new genes to the chicken linkage map. In addition, two genes were added to the chicken map by fluorescent in situ hybridization. As the map position of the human homologues of 13 of these genes is known, these markers extend the comparative map between chicken and man. Our results confirm and refine conserved regions between chicken and man on chicken chromosomes 2 and 7 and on linkage group E29C09W09. Furthermore, an additional conserved region is identified on chromosome 7.

Radiosensitivity of human melanoma spheroids influenced by growth rate

The radiosensitivity of human melanoma cell line BRO was investigated using the multicellular tumor spheroid system. By adding different concentrations of bovine serum to the tissue culture medium, two different growth rates could be obtained. Spheroids (200-250 microns) were irradiated with graded single doses of X rays (2-8 Gy). The radiation response was quantified using specific growth delay, clonogenic cell survival, and spheroid cure. All three assays showed a growth rate dependent radiation response. At both growth rates the spheroid growth fraction and critical cell number were of comparable magnitude. There was a strong correlation between the radiation response of spheroid regenerating units and clonogenic cells from dispersed spheroids. Cell survival curves indicated a decreased ability to accumulate sublethal damage in fast growing multicellular tumor spheroids. From this study it appears that the intrinsic radiosensitivity of human melanoma cell line BRO cells in multicellular spheroids is modulated by intratumoral conditions.

Repair of sublethal damage in two human tumor cell lines grown as multicellular spheroids

Multicellular tumor spheroids (MTS) provide a suitable in vitro model to study radiation sensitivity of tumor cells. Two cell lines of human origin, obtained from a neuroblastoma (NB-100) and a squamous cell carcinoma (HN-1), were exposed to graded doses (4-9 Gy) of radiation with 18 MV photons. Radiation was applied either as a single or as a split dose with an interval of 6 hr to determine the extent of sublethal damage repair. Treated spheroids regrew at approximately the same growth rate as control multicellular tumor spheroids, preceded by a static or regression phase. Radiation response was quantified in terms of regrowth delay, expressed as the time needed for treated spheroids to obtain an 8-fold increase of the initial volume at the time of irradiation. Data obtained from regrowth delay analysis were used to calculate the extent of sublethal damage repair, showing for the squamous cell carcinoma line a fractionally higher capacity to repair sublethal damage than the neuroblastoma line. Repair increased with larger dose fractions in both cell lines. Our results show that multicellular tumor spheroids from the two cell lines used in this study are best applicable at relatively high total radiation doses. This makes multicellular tumor spheroids a suitable model for the in vitro evaluation of clinical treatment rationales such as hyperfractionation.

Cell lines of human oral squamous-cell carcinomas retaining their differentiated phenotype

Two cell lines from head-and-neck squamous-cell carcinomas (SCC) have been established and characterized. Cell line R105 was derived from a xenografted SCC of the floor of the mouth and cell line T87/rc from a SCC of the epiglottis. Identification of individual cytokeratins 4, 5, 7, 8, 10, 13, 14, 18 and 19 led to the conclusion that both cell types had squamous characteristics and that keratinization occurred in xenografts. Ultrastructurally, junctional complexes were observed in both cell lines. Characteristic marker chromosomes were found and although both cell lines were derived from male patients, the Y chromosome was missing from all examined cells. The basic biological parameters of both cell lines were modal chromosome numbers of 59 (R105) and 60 (T87/rc), a doubling time of 60 (R105) and 45 hr (T87/rc) and a DNA index of 1.54 (R105) and 1.31 (T87/rc). The tumorigenicity of the 2 cell lines was proved by the ability to form colonies on a plastic substratum, as well as in a soft agar assay. Furthermore, the cells could produce multi-cellular tumour spheroids, and formed tumour nodules after subcutaneous inoculation into nude mice. The R105 tumour cells appeared to be better differentiated than the T87/rc as observed by histology and immuno(histo)chemistry. Both cell lines appear to retain SCC differentiation after being xenografted into nude mice, cultured for more than 40 passages in vitro and thereafter again xenografted into nude mice.

Sublethal damage repair and radiosensitivity of human squamous cell carcinoma cells grown with different culture techniques

In this study, cells of a human squamous cell carcinoma line, HN-1, were grown in monolayers and as multicellular tumour spheroids (MTS). Repair of radiation-induced damage was studied by irradiation with single and split doses of X rays (4-8 Gy). It was shown that the amount of sublethal damage that was repaired in this dose range was equal in cells growing in monolayers and as MTS. The radiosensitivity of spheroids, as expressed by spheroid "cure" dose, increased with increasing MTS diameter. It is postulated that, in MTS with no signs of hypoxia, radioresistance diminishes when MTS increase in diameter.

Sublethal damage repair in two radioresistant human tumor cell lines irradiated as multicellular spheroids

Melanoma and lung adenocarcinoma may be amenable for radiotherapy if it were possible to increase the presently used total dose. In order to investigate this, spheroids from two cell lines of human origin, one obtained from a BRO melanoma and one from an NCI-H125 lung adenocarcinoma were exposed to graded doses (3-9 Gy) of radiation with 18-MV photons. Radiation was applied either as a single dose or as split doses with an interval of 6 h to determine the extent of sublethal damage repair. Radiation response was quantified in terms of spheroid cure and specific growth delay. Both cells lines have previously been shown to be less sensitive than a neuroblastoma and a squamous cell carcinoma cell line grown as spheroids. Data obtained from the growth delay analysis were used to calculate the extent of split-dose recovery. Repaired dose for BRO spheroids did not increase after 7 Gy, whereas in NCI-H125, the repaired dose showed a steady increase. Recovery ratios did not differ between the two cell lines, but were lower than reported for normal tissues. Both cell lines revealed a low repair capacity was expressed by the beta-value of the linear-quadratic (LQ) equation. However, repair capacity for sublethal damage as expressed by the dose repaired and the beta-value of the LQ equation was not different from values reported earlier by us for neuroblastoma and squamous cell carcinoma when grown as spheroids. This indicates that the low radiosensitivity for the cell lines used in this study is determined by the alpha-value of the LQ equation. Our results support the clinical finding that the application of increased total radiation doses in the treatment of melanoma and lung adenocarcinoma may be feasible if radiation is applied in multiple small fractions to ensure normal tissue sparing.