Chemical extraction methods to assess bioavailable arsenic in soil and solid media.

Soil ingestion by children is an important pathway in assessing public health risks associated with exposure to arsenic-contaminated soils. Soil chemical methods are available to extract various pools of soil arsenic, but their ability to measure bioavailable arsenic from soil ingestion is unknown. Arsenic extracted by five commonly used soil extractants was compared with bioavailable arsenic measured in vivo by immature swine (Sus scrofa) dosing trials. Fifteen contaminated soils that contained 233 to 17 500 mg kg(-1) arsenic were studied. Soil extractants were selected to dissolve surficially adsorbed and/or readily soluble arsenic (water, 1 M sodium acetate, 0.1 M Na2HPO4/0.1 M NaH2PO4) and arsenic in Fe and Mn oxide minerals (hydroxylamine hydrochloride, ammonium oxalate). The mean percent of total arsenic extracted was: ammonium oxalate (53.6%) > or = hydroxylamine hydrochloride (51.7%) > phosphate (10.5%), acetate (7.16%) > water (0.15%). The strongest relationship between arsenic determined by soil chemical extraction and in vivo bioavailable arsenic was found for hydroxylamine hydrochloride extractant (r = 0.88, significant at the 0.01 probability level). Comparison of the amount of arsenic extracted by soil methods with bioavailable arsenic showed the following trend: ammonium oxalate, hydroxylamine hydrochloride > in vivo > phosphate, acetate > water. The amount of arsenic dissolved in the stomach (potentially bioavailable) is between surficially adsorbed (extracted by phosphate or acetate) and surficially adsorbed + nonsurficial forms in Fe and Mn oxides (extracted by hydroxylamine hydrochloride or ammonium oxalate). Soil extraction methods that dissolve some of the amorphous Fe, such as hydroxylamine hydrochloride, can be designed to provide closer estimates of bioavailable arsenic.

FISH assessment of aneuploidy frequencies in mature and immature human spermatozoa classified by the absence or presence of cytoplasmic retention.

Previously, a relationship has been found between diminished cellular maturity of human spermatozoa and low-level expression of the testis-specific chaperone protein, HspA2. Because HspA2 is a component of the synaptonemal complex in rodents, and assuming that this is also the case in men, it was postulated that the frequency of chromosomal aneuploidies would be higher in immature versus mature spermatozoa. This question was examined in spermatozoa from semen and from 80% Percoll pellets (enriched for mature spermatozoa) of the same ejaculate in 10 oligozoospermic men. Immature spermatozoa with retained cytoplasm, which signifies spermiogenetic arrest, were identified by immunocytochemistry. Using fluorescence in-situ hybridization (FISH), approximately 7000 sperm nuclei were evaluated in each of the 20 fractions (142 086 spermatozoa in all) using centromeric probes for the X, Y and 17 chromosomes. The proportions of immature spermatozoa were 45.4 +/- 3.4 versus 26.6 +/- 2.2% in the two semen versus the Percoll groups (medians: 48.2 versus 25%, P < 0.001, n = 300 spermatozoa per fraction, total 6000 spermatozoa). There was also a concomitant decline in total disomy, total diploidy and total aneuploidy frequencies in the 80% Percoll versus semen fractions (0.17 versus 0.54%, 0.14 versus 0.26% and 0.31 versus 0.81% respectively, P < 0.001 in all comparisons). The mean decline of aneuploidies was 2.7-fold. With regard to the hypothesis that aneuploidies are related to sperm immaturity, there was a close correlation between the incidence of immature spermatozoa and disomies (r = 0.7, P < 0.001) but no correlation with diploidies (r = 0.03), indicating that disomies originate primarily in immature spermatozoa. It is suggested that the common factor underlying sperm immaturity and aneuploidies is the diminished expression of HspA2. In addition, the lack of this chaperone may also cause diminished cellular transport of proteins, such as DNA-repair enzymes or of the retention of cytoplasm that is extruded from normally maturing spermatozoa during spermiogenesis.

Small marker chromosome identification in metaphase and interphase using centromeric multiplex fish (CM-FISH).

Multicolor karyotyping procedures, such as multiplex fluorescence in situ hybridization (M-FISH), spectral karyotyping, or color-changing karyotyping, can be used to detect chromosomal rearrangements and marker chromosomes in prenatal diagnosis, peripheral blood cultures, leukemia, and solid tumors, especially in cases where G-banding is not sufficient. A regular M-FISH analysis requires relatively large amounts of labeled DNA (microgram quantities), is not informative in interphase nuclei, hybridization can take up to 2 to 3 days, and unlabeled human chromosome-painting probes are not available commercially. Unique probes (plasmids, PAC), specific for centromeric or subtelomeric chromosomal regions, can replace the painting probes in M-FISH to address specific issues, such as the identification of marker chromosomes and aneuploidies. A set of plasmid probes carrying repetitive sequences specific for the alpha-satellite region of all human chromosomes were combined in a metaphase assay and an interphase assay, allowing identification of aneuploidies in one hybridization step, on a single cytogenetic slide. The fluorophore-dUTP and the labeled antibodies required to label and detect the DNA probes can be prepared in any laboratory. All DNA probes can be easily isolated and labeled using common molecular cytogenetic procedures. Because of the repetitive nature of the probes, hybridization time is short, usually less than 1 hour, and the analysis can be performed with nonspecialized image-processing software.

Cryptic translocation identification in human and mouse using several telomeric multiplex fish (TM-FISH) strategies.

Experimental data published in recent years showed that up to 10% of all cases of mild to severe idiopathic mental retardation may result from small rearrangements of the subtelomeric regions of human chromosomes. To detect such cryptic translocations, we developed a "telomeric" multiplex fluorescence in situ hybridization (M-FISH) assay, using a set of previously published and commercially available subtelomeric probes. This set of probes includes 41 cosmid/PAC/P1 clones located from less than 100 kilobases to approximately 1 megabase from the end of the chromosomes. Similarly, a published mouse probe set, comprised of BACs hybridizing to the closest known marker toward the centromere and telomere of each mouse chromosome, was used to develop a mouse-specific "telomeric" M-FISH. Three different combinatorial labeling strategies were used to simultaneously detect all human subtelomeric regions on one slide. The simplest approach uses only three fluors and can be performed in laboratories lacking sophisticated imaging equipment or personnel highly trained in cytogenetics. A standard fluorescence microscope equipped with only three filters is sufficient. Fluor-dUTPs and labeled probes can be custom made, thus dramatically reducing costs. Images can be prepared using imaging software (Adobe Photoshop) and analysis performed by simple visual inspection.

Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification.

Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can be exploited to visualize single molecular recognition events. Here we report the use of RCA to visualize target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Three unique target sequences within the cystic fibrosis transmembrane conductance regulator gene could be detected simultaneously in interphase nuclei, and could be ordered in a linear map in stretched DNA. Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis transmembrane conductance regulator, p53, BRCA-1, and Gorlin syndrome genes in the nuclei of cultured cells or in DNA fibers. These observations demonstrate that signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules. This provides a means for direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis.

Signaling by toll-like receptor 2 and 4 agonists results in differential gene expression in murine macrophages.

Lipopolysaccharide (LPS) derived from the periodontal pathogen Porphyromonas gingivalis has been reported to differ structurally and functionally from enterobacterial LPS. These studies demonstrate that in contrast to protein-free enterobacterial LPS, a similarly purified preparation of P. gingivalis LPS exhibited potent Toll-like receptor 2 (TLR2), rather than TLR4, agonist activity to elicit gene expression and cytokine secretion in murine macrophages and transfectants. More importantly, TLR2 stimulation by this P. gingivalis LPS preparation resulted in differential expression of a panel of genes that are normally induced in murine macrophages by Escherichia coli LPS. These data suggest that (i) P. gingivalis LPS does not signal through TLR4 and (ii) signaling through TLR2 and through TLR4 differs quantitatively and qualitatively. Our data support the hypothesis that the shared signaling pathways elicited by TLR2 and by TLR4 agonists must diverge in order to account for the distinct patterns of inflammatory gene expression.

Improvements in cytogenetic slide preparation: controlled chromosome spreading, chemical aging and gradual denaturing.

BACKGROUND: Metaphase spreading is an essential technique for clinical and molecular cytogenetics. Results of classical banding techniques as well as complex fluorescent in situ hybridization (FISH) applications, such as comparative genomic hybridization (CGH) or multiplex FISH (M-FISH), are greatly influenced by the quality of chromosome spreading and pretreatment of the slide prior to hybridization. Materials and Methods Using hot steam and a metal plate with a temperature gradient across its surface, a reproducible protocol for slide preparation, aging, and hybridization was developed. RESULTS: This protocol yields good chromosome spreads from even the most difficult cell suspensions and is unaffected by the environmental conditions. Chromosome spreads were suitable for both banding and FISH techniques common to the cytogenetic laboratory. Chemical aging is a rapid slide pretreatment procedure for FISH applications, which allows freshly prepared cytogenetic slides to be used for in situ hybridization within 30 min, thus increasing analytical throughput and reducing benchwork. Furthermore, the gradually denaturing process described allows the use of fresh biologic material with optimal FISH results while protecting chromosomal integrity during denaturing. CONCLUSION: The slide preparation and slide pretreatment protocols can be performed in any laboratory, do not require specialized equipment, and provide robust results.

Cloning and characterization of two mouse genes with homology to the yeast Sir2 gene.

The yeast Sir2 gene encodes a protein (Sir2p) that plays an essential role in silencing regulation at mating-type loci, rDNA, and telomeres. Recent studies have also shown that the protein participates in cell cycle regulation, DNA double-strand break repair, meiotic checkpoint control, and histone deacetylation. Overexpression of wildtype Sir2p in yeast resulted in an extended life span but mutant Sir2p shortened the life span, suggesting its function in aging processes. Sir2p is evolutionarily conserved from prokaryotes to higher eukaryotes. However, its function(s) in mammals remains unknown. To investigate Sir2p function(s) in mice, we cloned and characterized two mouse Sir2-like genes. Our results revealed that the two mouse Sir2-like proteins (mSIR2L2 and mSIR2L3) are most similar to the human Sir2-like proteins SIR2L2 and SIR2L3, respectively. Sir2 core domains are highly conserved in the two proteins and yeast Sir2p; however, the intracellular localizations of both mSIR2L2 and mSIR2L3 differ from that of yeast Sir2p and from one another. The two mouse genes have completely different genomic structures but were mapped on the same chromosome. It seems that the two mouse proteins, though they have Sir2 conserved domains, may function differently than yeast Sir2p.

Comparative genomic hybridization of fine needle aspirates from breast carcinomas.

Detailed knowledge of chromosomal aberrations in a specific tumor may facilitate the development of individually tailored chemotherapy, hormone or gene therapy. Unfortunately, karyotype analysis requires living cells and is complicated by the low number of good metaphase spreads obtained. Comparative genomic hybridization (CGH), however, is capable of detecting and mapping genome-wide amplifications and deletions using an equimolar mixture of normal and tumor cell DNA. We show here that even the few cells from a fine needle aspirate of a tumor are sufficient for a direct CGH assay, independent of DNA amplification. Ten primary breast cancers were analyzed by CGH. A fresh frozen fine needle aspirate and a formalin-fixed and paraffin-embedded section were used for each tumor. Metaphases from each CGH reaction were imaged, and a sum ratio profile was determined for every chromosome. The ratio profiles of DNA isolated from the 2 material sources were then compared. Fine needle aspirates and the paraffin-embedded material of a single tumor yielded the same fluorescence ratio profiles, albeit with slightly different confidence intervals. Different tumors showed a variety of aberrations. The most frequently observed changes were 1q+, 8q+, 14q-, 16p+, 16q-, 17p-, 17q+, 19q+, 20q+, 21q- and 22q-. The ability of CGH to assess chromosomal changes in breast cancer from fine needle aspirates could facilitate genetic evaluation of tumors prior to surgery.

Numerical aberrations of chromosomes 1 and 17 correlate with tumor site in human gastric carcinoma of the diffuse and intestinal types. Fluorescence in situ hybridization analysis on gastric biopsies.

Recent studies predict that tumor aneuploidy plays a direct role in tumor instability. The relationship between interphase cytogenetics, histology, grade, and tumor site was analyzed in 20 primary gastric carcinomas. Using fluorescence in-situ hybridization, the numerical changes of centromeric sequences of chromosomes 1, 3, 10, and 17 were directly analyzed in gastric biopsies. Polysomic copy numbers of chromosomes 1 and 17 were discovered in 63% (10 of 16) and 59% (10 of 17), respectively, of informative cancer cases. Chromosome 3 and 10 signal number changes were found in only 6% (1 of 16) and 13% (1 of 8), respectively, of informative cancer cases. There was a positive correlation between the appearance of polysomic nuclear target sites of chromosomes 1 and 17 (correlation coefficient r = 0.72; p < 0.005). Copy number changes were not significantly related to histologic subtypes of either the Laurén or WHO classifications. However, incidence of cancers having dual polysomic signal number abnormalities for both chromosomes 1 and 17 was significantly correlated to tumor location at the cardia. The data suggests that (i) human gastric cancer appears in two genomic groups that can be reliably diagnosed by fluorescence in-situ hybridization on routine biopsy sections, (ii) numerical aberrations of chromosomes 1, 3, 10, and 17 are largely independent of histologic subtypes, and (iii) polysomic copy number abnormalities of chromosomes 1 and 17 correlate to intragastric tumor site and are highest in cardia cancers, suggesting high tumor instability at this particular location.

Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection.

We describe an adaptation of the rolling circle amplification (RCA) reporter system for the detection of protein Ags, termed "immunoRCA. " In immunoRCA, an oligonucleotide primer is covalently attached to an Ab; thus, in the presence of circular DNA, DNA polymerase, and nucleotides, amplification results in a long DNA molecule containing hundreds of copies of the circular DNA sequence that remain attached to the Ab and that can be detected in a variety of ways. Using immunoRCA, analytes were detected at sensitivities exceeding those of conventional enzyme immunoassays in ELISA and microparticle formats. The signal amplification afforded by immunoRCA also enabled immunoassays to be carried out in microspot and microarray formats with exquisite sensitivity. When Ags are present at concentrations down to fM levels, specifically bound Abs can be scored by counting discrete fluorescent signals arising from individual Ag-Ab complexes. Multiplex immunoRCA also was demonstrated by accurately quantifying Ags mixed in different ratios in a two-color, single-molecule-counting assay on a glass slide. ImmunoRCA thus combines high sensitivity and a very wide dynamic range with an unprecedented capability for single molecule detection. This Ag-detection method is of general applicability and is extendable to multiplexed immunoassays that employ a battery of different Abs, each labeled with a unique oligonucleotide primer, that can be discriminated by a color-coded visualization system. ImmunoRCA-profiling based on the simultaneous quantitation of multiple Ags should expand the power of immunoassays by exploiting the increased information content of ratio-based expression analysis.

Cytogenetical diagnosis in paraffin-embedded fetoplacental tissue using comparative genomic hybridization.

Comparative genomic hybridization (CGH) is a FISH-related technique used to assess global chromosomal aberrations in a variety of human tumours. Recently CGH has been applied to cytogenetic analysis of fresh frozen fetoplacental tissues. Here we report the application of CGH to paraffin-embedded placental samples. Ten samples from paraffin-embedded blocks of 6 control placentas and fetoplacental tissue from 10 aneuploidies, and 2 unbalanced aberrations were evaluated. Balanced karyotype profiles were obtained from samples of healthy placentas and all samples from the same placenta appeared to have similar confidence intervals. CGH analysis of four cases of trisomy 21, three cases of trisomy 18, one case of trisomy 13, one case of trisomy 15 and one case of trisomy 7 all showed overrepresentation of the respective trisomic chromosome. The CGH profile was also in accordance with the karyotyping of a case with isochromosome 21. The CGH profile of a case with der (2)t(2;6)(q37.3;q22.2) revealed partial trisomy for chromosome 6 between q21 and q27. CGH may be a useful adjunct in prenatal genetic diagnosis when retrospective diagnosis is needed from archival samples.

Custom fluorescent-nucleotide synthesis as an alternative method for nucleic acid labeling.

The variety of potentially useful dyes or haptenes available for fluorescent nucleic acid hybridization assays is far greater than what can be obtained from commercial sources. Since this diversity could be useful in many laboratory applications, we have developed a simple and inexpensive procedure for preparing nonpurified labeled nucleotides, for use in common nucleic acid labeling reactions, such as PCR and nick translation. The modified nucleotides were synthesized by coupling allylamine-dUTP to the succinimidyl-ester derivatives of the fluorescent dyes or haptenes such as biotin or digoxigenin, which require fluorescently labeled proteins for detection. This method allows custom preparation of most common fluorescent nucleotides and rapid testing of new ones, while reducing the cost of procedures such as multiplex fluorescent in situ hybridization (M-FISH) by 100-200 fold.

Simple method for preparation of fluor/hapten-labeled dUTP.

Many projects, such as multiplex-fluorescence in situ hybridization (M-FISH) karyotyping, require the use of relatively large amounts of multiple fluor- or hapten-labeled nucleotides for the preparation of DNA probes. Such a requirement makes these experimental approaches prohibitively expensive for many researchers. The cost of such nucleotides can be reduced approximately 99% by purchasing the chemical precursors, fluor or hapten succinimidyl esters and 5-(3-aminoallyl)-2'-deoxyuridine 5' triphosphate (AA-dUTP), and performing the simple coupling/purification described here. It is possible to finish four to ten different fluor/hapten dUTP preparations of 2.5 microM scale within a 24 h period. The reagent cost for each preparation ranges from $33-$237 per microM, depending on the fluor/hapten. This laboratory uses such nucleotide preparations to prepare FISH probes by nick translation or PCR amplification.

Genomic organization and chromosomal localization of the murine 2 P domain potassium channel gene Kcnk8: conservation of gene structure in 2 P domain potassium channels.

A 2 P domain potassium channel expressed in eye, lung, and stomach, Kcnk8, has recently been identified. To initiate further biochemical and genetic studies of this channel, we assembled the murine Kcnk8 cDNA sequence, characterized the genomic structure of the Kcnk8 gene, determined its chromosomal localization, and analyzed its activity in a Xenopus laevis oocyte expression system. The composite cDNA has an open reading frame of 1029 bp and encodes a protein of 343 amino acids with a predicted molecular mass of 36 kDa. Structure analyses predict 2 P domains and four potential transmembrane helices with a potential single EF-hand motif and four potential SH3-binding motifs in the COOH-terminus. Cloning of the Kcnk8 chromosomal gene revealed that it is composed of three exons distributed over 4 kb of genomic DNA. Genome database searching revealed that one of the intron/exon boundaries identified in Kcnk8 is present in other mammalian 2 P domain potassium channels genes and many C. elegans 2P domain potassium channel genes, revealing evolutionary conservation of gene structure. Using fluorescence in situ hybridization, the murine Kcnk8 gene was mapped to chromosome 19, 2B, the locus of the murine dancer phenotype, and syntenic to 11q11-11q13, the location of the human homologue. No significant currents were generated in a Xenopus laevis oocyte expression system using the composite Kcnk8 cDNA sequence, suggesting, like many potassium channels, additional channel subunits, modulator substances, or cellular chaperones are required for channel function.