The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.

Structural variation in the human genome

The near-field optical interaction between a sharp probe and a sample of interest can be exploited to image, spectroscopically probe, or modify surfaces at a resolution (down to ∼12 nm) inaccessible by traditional far-field techniques. Many of the attractive features of conventional optics are retained, including noninvasiveness, reliability, and low cost. In addition, most optical contrast mechanisms can be extended to the near-field regime, resulting in a technique of considerable versatility. This versatility is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall, magneto-optic domains having implications for highdensity data storage. Although the technique may find uses in many diverse fields, two of the most exciting possibilities are localized optical spectroscopy of semiconductors and the fluorescence imaging of living cells.

https://science.sciencemag.org/content/sci/257/5067/189.full.pdf

Near-Field Optics: Microscopy, Spectroscopy, and Surface Modification Beyond the Diffraction Limit

Members of the recently recognized SRC-1 family of transcriptional coactivators interact with steroid hormone receptors to enhance ligand-dependent transcription. AIB1, a member of the SRC-1 family, was cloned during a search on the long arm of chromosome 20 for genes whose expression and copy number were elevated in human breast cancers. AIB1 amplification and overexpression were observed in four of five estrogen receptor-positive breast and ovarian cancer cell lines. Subsequent evaluation of 105 unselected specimens of primary breast cancer found AIB1 amplification in approximately 10 percent and high expression in 64 percent of the primary tumors analyzed. AIB1 protein interacted with estrogen receptors in a ligand-dependent fashion, and transfection of AIB1 resulted in enhancement of estrogen-dependent transcription. These observations identify AIB1 as a nuclear receptor coactivator whose altered expression may contribute to development of steroid-dependent cancers.

/pdf/aib1-a-steroid-receptor-coactivator-amplified-in-breast-and-1j7n2b8wjh.pdf

AIB1, a Steroid Receptor Coactivator Amplified in Breast and Ovarian Cancer

https://academiccommons.columbia.edu/doi/10.7916/D8NC6C9K/download

Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RARα with a novel putative transcription factor, PML

Chromosomes can be specifically stained in metaphase spreads and interphase nuclei by in situ hybridization with entire chromosome-specific DNA libraries. Unlabeled human genomic DNA is used to inhibit the hybridization of sequences in the library that bind to multiple chromosomes. The target chromosome can be made at least 20 times brighter per unit length than the others. Trisomy 21 and translocations involving chromosome 4 can be detected in metaphase spreads and interphase nuclei by using this technique.

https://www.pnas.org/content/pnas/85/23/9138.full.pdf

Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4.

This report describes the use of fluorescence in situ hybridization for chromosome classification and detection of chromosome aberrations. Biotin-labeled DNA was hybridized to target chromosomes and subsequently rendered fluorescent by successive treatments with fluorescein-labeled avidin and biotinylated anti-avidin antibody. Human chromosomes in human-hamster hybrid cell lines were intensely and uniformly stained in metaphase spreads and interphase nuclei when human genomic DNA was used as a probe. Interspecies translocations were detected easily at metaphase. The human-specific fluorescence intensity from cell nuclei and chromosomes was proportional to the amount of target human DNA. Human Y chromosomes were fluorescently stained in metaphase and interphase nuclei by using a 0.8-kilobase DNA probe specific for the Y chromosome. Cells from males were 40 times brighter than those from females. Both Y chromosomal domains were visible in most interphase nuclei of XYY amniocytes. Human 28S ribosomal RNA genes on metaphase chromosomes were distinctly stained by using a 1.5-kilobase DNA probe.

https://www.pnas.org/content/pnas/83/9/2934.full.pdf

Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization.

Thisreport describes theuseoffluorescence insitu hybridization forchromosome classification anddetec- tionofchromosome aberrations. Biotin-labeled DNA was hybridized totarget chromosomes andsubsequently rendered fluorescent bysuccessive treatments withfluorescein-labeled avidin andbiotinylated anti-avidin antibody. Humanchromo- somes inhuman-hamster hybrid cell lines wereintensely and uniformly stained inmetaphase spreads andinterphase nuclei whenhumangenomic DNAwasusedasaprobe. Interspecies translocations weredetected easily atmetaphase. Thehuman- specific fluorescence intensity fromcell nuclei andchromo- somes wasproportional totheamount oftarget humanDNA. HumanY chromosomes werefluorescently stained inmeta- phase andinterphase nuclei byusing a0.8-kilobase DNAprobe specific fortheYchromosome. Cells frommales were40times brighter thanthose fromfemales. BothY chromosomal do- mainswerevisible inmostinterphase nuclei ofXYY amniocytes. Human28Sribosomal RNAgenes onmetaphase chromosomes weredistinctly stained byusing a1.5-kilobase DNAprobe.

Cytogenetic analysis using quantitative, high-sensitivity

Dual color FISH with whole chromosome and pan-centromere probes facilitates rapid detection of stable structural aberrations such as translocations. This approach should allow analysis of translocations for assessment of genetic damage at long times after exposure or as a result of chronic exposure during a long period of time. Multi-color FISH with locus specific probes allows assessment of the frequency of cells carrying specific aberrations known to be associated with tumorigenesis, analysis of the series of genetic changes that occur during tumor evolution and correlation between genotype and phenotype. The power of FISH for analysis of random and tumor related events will increase steadily as informative probes are developed during the course of the International Human Genome Project.

Applications of fluorescence in situ hybridization in biological dosimetry and detection of disease-specific chromosome aberrations.

ABSTRACT
The objective of this paper is to evaluate the accuracy of the NASA BioSentinel Pixel Dosimeter (BPD) using gamma-ray and neutron sources in a standard calibration lab. The dosimeter tested here is the ground-based version of the BPD that will be onboard the BioSentinel mission. The BPD was exposed to radiation from 60Co, 137Cs, and 252Cf at selected distances (dose rates) at the Lawrence Livermore National Laboratory (LLNL) Radiation Calibration Laboratory (RCL), and the results were compared with NIST traceable benchmark values. It is recognized that these sources are not analogs for the space environment but do provide direct comparisons between BPD response and well characterized calibration lab values. For gamma rays, the BPD measured absorbed dose agrees to ≤ 3.8% compared with RCL benchmark values. For neutrons, the results show that the BPD is insensitive, i.e., the BPD detected only the gamma-ray dose component from 252Cf. The LET spectra obtained for gamma rays from 60Co and 252Cf are consistent with expectations for these gamma-ray energies, but the LET spectrum from the 137Cs gamma rays differs substantially. The potential causes for this difference are the high dose rate from 137Cs and the lower secondary electron energy produced by 137Cs gamma rays. However, neither of these results in errors in the absorbed dose. Based on comparisons with NIST-traceable standards, it is evident that the BPD can measure absorbed dose accurately from low LET charged particles. The sensor's insensitivity to neutrons is unlikely to be a limitation for the BioSentinel mission due to the expected low secondary neutron fluence.

Testing the NASA BioSentinel Pixel Dosimeter Using Gamma-ray and Neutron Sources at the LLNL Calibration Lab.

Radiation-induced biological damage results in formation of a broad spectrum of cytogenetic changes such as translocations, dicentrics, ring chromosomes, and acentric fragments. A battery of analytical cytologic techniques are now emerging that promise to significantly improve the precision and ease with which these radiation induced cytogenetic changes can be quantified. This report summarizes techniques to facilitate analysis of the frequency of occurrence of structural and numerical aberrations in control and irradiated human cells. 14 refs., 2 figs.

/pdf/analytical-cytology-applied-to-detection-of-induced-351w6g3o0q.pdf

T. Straume

Papers

Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization.

Cytogenetic analysis using quantitative, high-sensitivity

Applications of fluorescence in situ hybridization in biological dosimetry and detection of disease-specific chromosome aberrations.

Testing the NASA BioSentinel Pixel Dosimeter Using Gamma-ray and Neutron Sources at the LLNL Calibration Lab.

Analytical cytology applied to detection of induced cytogenetic abnormalities