Multiplexed microsatellite recovery using massively parallel sequencing.

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

Parentage and relatedness in polyandrous comb-crested jacanas using ISSRs.

In this article we present the first analysis of parentage and relatedness in a natural vertebrate population, using Intersimple Sequence Repeat (ISSR) markers. Thus, 28 ISSR markers were used in a study of a sex-role reversed, simultaneously polyandrous shorebird from northeastern Australia, the comb-crested jacana (Irediparra gallinacea). Assessment of parentage was based on comparison of field observations, novel bands, individual-specific bands found in 7/9 males and 4/6 females, and a 99% CI exclusion criteria. Integrating results from these approaches resulted in confirmation of paternity in all 36 chicks. In only one case (2.8% of chicks) was a co-mate assigned paternity. Thus, comb-crested jacanas appear to be genetically monogamous. These results showed resemblance to sequentially polyandrous birds but differed from the simultaneously polyandrous wattled jacana ( Jacana jacana; Emlen et al. 1998). A significant relationship between relatedness and ISSR similarity resulted in recognition that 14/15 adults sampled may be related to at least one other adult by 0.25 or more. Lack of dispersal may be explained by physical limitations and adequate regional habitat. ISSRs proved to be simple and helpful in resolving these issues.

Somatic delivery of catecholamines in the striatum attenuate parkinsonian symptoms and widen the therapeutic window of oral sinemet in rats.

Guidelines for clinical transplantation studies for Parkinson's disease emphasize that transplants should be considered as an adjunct to systemic L-DOPA, yet few preclinical studies have specifically assessed the potential of transplants as an adjunct to the clinical gold standard treatment. The objectives of the present study were to determine if encapsulated PC12 cells implanted in rats with severe unilateral dopamine depletions: (i) have a direct therapeutic effect on measures of parkinsonian symptoms; and/or (ii) increase the therapeutic window of oral sinemet in this model. Rats with severe unilateral dopamine depletions received striatal implants of encapsulated PC12 cells producing dopamine and L-DOPA. These rats were tested on a battery of behavioral measures of parkinsonian symptoms, at a range of doses of oral sinemet (0, 12, 24, and 36 mg/kg). Stereotypies/dyskinesias were also quantified after high doses of oral sinemet (36 and 50 mg/kg). The results confirm that parkinsonian symptoms can be quantified in rats with severe dopamine depletions, and the validity and clinical relevance of these measures are supported by the fact that the clinical gold standard treatment, oral sinemet, attenuates these parkinsonian symptoms. Somatic delivery of dopamine and L-DOPA, directly to the dopamine-depleted striatum, also attenuates parkinsonian symptoms. In fact, the magnitude of the therapeutic effect produced by continuous, site-specific, somatic delivery of dopamine and L-DOPA was larger than the effect produced by acute, systemic, oral sinemet. The beneficial effects of oral sinemet and striatal implants of catecholamine-producing devices were additive, but there were no adverse effects related to striatal catecholamine-producing devices, and these devices did not increase the adverse effects related to oral sinemet. Therefore, striatal implants of catecholamine-producing devices have direct therapeutic effects which are fairly robust, and they widen the therapeutic window of oral sinemet.

Ultrastructural differentiation of sodium butyrate-treated human pancreatic adenocarcinoma cell lines.

The differentiation effects of sodium butyrate were examined in a series of human pancreatic adenocarcinoma cell lines: Panc-1, a poorly differentiated cell line; HPAF, a pleomorphic cell line isolated in this laboratory; and two clones of the parental HPAF cell line, well-differentiated CD11 and less-differentiated CD18. Incubation with 2 mM sodium butyrate induced a dramatic decrease in cell proliferation and saturation densities in culture and an increase in alkaline phosphatase activity. Of particular interest, incubation with sodium butyrate also caused a number of morphologic alterations in these cells, attributed to an induction of secretory differentiation. Following sodium butyrate treatment, CD18 cells were virtually indistinguishable from the more highly differentiated CD11 cells as evidenced by an increase in the number of profiles of rough endoplasmic reticulum and of Golgi. Intercellular and intracytoplasmic lumens, whose appearance is quite common in CD11 cells but nonexistent in untreated CD18 cells, appeared in these cells following only 5 days of sodium butyrate treatment. An increase in the cytoplasmic secretory elements was also observed in sodium butyrate-treated Panc-1 cells; however, lumen formation never occurred in these cells.

Characterization of clones of a human pancreatic adenocarcinoma cell line representing different stages of differentiation.

With a limiting dilution technique, clones have been established from the human pancreatic adenocarcinoma cell line, HPAF. Phenotypic analysis by a panel of murine monoclonal antibodies demonstrated distinct profiles of antigenic expression between the clones. However, identical isozyme patterns of different clones indicated their common origin from the parental HPAF cells. Two clones, CD11 and CD18, appeared to be arrested at different stages of secretory epithelial cell differentiation. CD11 cells demonstrated many characteristics of a well-differentiated state, including the formation of ductal structures with polarized, long columnar-shaped cells, the presence of secretory granules in the cytoplasm, high DU-PAN-2 antigen expression in nude mouse xenografts, and a longer doubling time (42 h) in tissue culture. In contrast, CD18 cells exhibited characteristics of a poorly differentiated state, including solid nests of isoprismatic cells without luminal spaces and cellular polarization, absence of secretory granules and DU-PAN-2 antigen expression in xenografts, and a shorter doubling time (26 h) in tissue culture. Since no culture systems of normal pancreatic ductal cells are currently available, these two pancreatic adenocarcinoma clones may provide a unique system to study genes and antigens related to pancreatic ductal cell differentiation.

Selective inhibition of human ribosomal gene transcription by the morpholinyl anthracyclines cyanomorpholinyl- and morpholinyldoxorubicin.

Upon incubation of cultured mammalian cells with the new anthracycline analogues cyanomorpholinyldoxorubicin and morpholinyldoxorubicin, nucleoli irreversibly segregate into their substructures which form individual portions of the nucleolar mass and characteristic electron-dense components adjacent to the nucleolonema; these changes in nucleolar ultrastructure are similar to those produced by actinomycin D (AMD). In the present study we have examined the effects of anthracycline analogues on RNA synthesis, localization of RNA polymerase I in situ, and activity of RNA polymerases in vitro, and compared these effects with those of the parent compound doxorubicin (DOX) and AMD. The results show that, following treatment with cyanomorpholinyldoxorubicin, morpholinyldoxorubicin, and AMD, but not DOX, RNA polymerase I-containing transcription complexes were reduced, reflecting the transcriptional activity of the rRNA genes. The residual RNA polymerase-containing entities were redistributed into cap-like aggregates at the nucleolar periphery. Within 30 min of exposure to cyanomorpholinyldoxorubicin, morpholinyldoxorubicin, and AMD, but not DOX, a 75-90% inhibition of RNA polymerase I activity in situ and in vitro was observed. At this early time there was no significant inhibition of nucleoplasmic RNA labeling in situ or RNA polymerases II and III activities in vitro. At later times following reincubation in drug-free medium, inhibition of all three polymerases was observed. Impairment of RNA synthesis appeared to result from drug interaction with the DNA template rather than an interaction with RNA polymerase I itself. We conclude that the morpholinyl derivatives of DOX are preferential inhibitors of ribosomal gene transcription and that they may have a mechanism of action similar to that of AMD on rRNA synthesis.

Involvement of chromosome 7 in primary lung tumor and nonmalignant normal lung tissue.

By using the newly developed adhesive tumor cell culture system, we analyzed the chromosomal constitutions of primary lung tumor and nonmalignant normal lung tissue from 10 previously untreated patients with non-small cell lung cancer. Chromosomal analyses were successfully carried out in banded chromosome preparations from 10 tumor and 8 normal lung tissue samples. All analyzed tumor and normal lung tissue samples had a predominantly normal diploid chromosome number. However, there was at least one structural or numerical alteration in every tumor and lung tissue sample analyzed. Chromosomes 1, 3, 4, 6, 7, 8, 9, 12, 15, and 20 were more often involved in rearrangement. The most consistent finding was trisomy 7; 4 patients had trisomy 7 in both tumor and normal lung tissue, and another 2 had this anomaly in tumor tissue only. Of the 4 patients without trisomy 7, 2 had a homogeneously staining region in the short arm of chromosome 7 in tumor tissue. Phytohemagglutinin-stimulated peripheral blood lymphocytes from 7 patients, including 5 patients with trisomy 7 in tumor tissue, did not show trisomy 7. These cytogenetic data suggest that chromosome 7 may be associated with lung cancer development and that trisomy 7 may be the hallmark of premalignant changes, at least in a subgroup of patients with non-small cell lung cancer.

Effects of 3'-deamino-3'-(3-cyano-4-morpholinyl)doxorubicin and doxorubicin on the survival, DNA integrity, and nucleolar morphology of human leukemia cells in vitro.

The potential mechanisms of the extremely potent anthracycline analogue 3'-deamino-3'-(3-cyano-4-morpholinyl)doxorubicin (MRA-CN) have been compared with those of doxorubicin (DOX) by examination of drug effects on colony formation, macromolecular synthesis, DNA integrity, and ultrastructure of human leukemia cells in vitro. Following a 1-h exposure, MRA-CN was found to be 1400-fold more cytocidal than DOX which correlated with the drugs' inhibitory effects on DNA and total RNA synthesis. Treatment with MRA-CN resulted in a dose-dependent production of DNA interstrand cross-links as quantified by alkaline elution. One-h treatments with DOX or 3'-deamino-3'-(4-morpholinyl) doxorubicin (the non-cyano-containing analogue of MRA-CN) produced no DNA-DNA cross-links; rather they produced protein-concealed DNA single-strand breaks. After removal of MRA-CN, the DNA of KBM-3 cells displayed time-dependent fragmentation as indicated by rapid DNA filter elution during the pH 10 lysis step which preceded pH 12 elution. Within 4 h of MRA-CN exposure (10 nM, 1 h), 50% of the cellular DNA was in the lysis fraction. By 24 h, all the cellular DNA was in this fraction. MRA-CN (10 nM), 3'-deamino-3'-(4-morpholinyl)doxorubicin (1 microM), and actinomycin D (1 microM), but not DOX (3 mircroM), each produced distinctive nucleolar macrosegregation, indicating an effect on rRNA synthesis. The alpha-CN substituent on the morpholinyl moiety of MRA-CN appears to be responsible for the unique antitumor potency of this anthracycline. Nucleolar macrosegregation is probably associated with the morpholinyl moiety and is independent of the alpha-CN substituent.