Characterization of two marker chromosomes in a patient with acute nonlymphocytic leukemia by two-color fluorescence in situ hybridization

A patient with acute nonlymphocytic leukemia (ANLL), M5b according to French-American-British (FAB) classification, showed monosomy 16, an extra 1p−, and a 21q+. These derivative chromosomes could not be defined by GTG-banding. For better characterization, we performed two-color fluorescence in situ hybridization (FISH) experiments applying DNA libraries from sorted human chromosomes, chromosome-specific repetitive probes, and a band-specific YAC-clone. With these FISH studies the karyotype could be characterized as 46,XY,+der(1)t(1;21)(p11;?),−16,der(21)t(16;21)(p11.1;q22)

Comparative chromosome band mapping in primates byin situ suppression hybridization of band specific DNA microlibraries

A DNA-library established from microdissected bands 8q23 to 8q24.1 of normal human chromosomes 8 (Lüdecke et al., 1989) was used as a probe for chromosomal in situ suppression (CISS-) hybridization to metaphase chromosomes of man and primates including Hylobates lar and Macaca fuscata. Comparative band mapping as first applied in this study shows the specific visualization of a single subchromosomal region in all three species and thus demonstrates that synteny of the bulk sequences of a specific human chromosome subregion has been conserved for more than 20 million years

Tidally Driven Processes Leading to Near-Field Turbulence in a Channel at the Crest of the Mendocino Escarpment*

In situ observations of tidally driven turbulence were obtained in a small channel that transects the crest of the Mendocino Ridge, a site of mixed (diurnal and semidiurnal) tides. Diurnal tides are subinertial at this latitude, and once per day a trapped tide leads to large flows through the channel giving rise to tidal excursion lengths comparable to the width of the ridge crest. During these times, energetic turbulence is observed in the channel, with overturns spanning almost half of the full water depth. A high-resolution, nonhydrostatic, 2.5-dimensional simulation is used to interpret the observations in terms of the advection of a breaking tidal lee wave that extends from the ridge crest to the surface and the subsequent development of a hydraulic jump on the flanks of the ridge. Modeled dissipation rates show that turbulence is strongest on the flanks of the ridge and that local dissipation accounts for 28% of the energy converted from the barotropic tide into baroclinic motion.United States. Office of Naval Research (Grant ONR N00014- 12-1-0943)National Science Foundation (U.S.). (Grant NSF OCE 1129763

A large field CCD system for quantitative imaging of microarrays

We describe a charge-coupled device (CCD) imaging system for microarrays capable of acquiring quantitative, high dynamic range images of very large fields. Illumination is supplied by an arc lamp, and filters are used to define excitation and emission bands. The system is linear down to fluorochrome densities ≪1 molecule/µm(2). The ratios of the illumination intensity distributions for all excitation wavelengths have a maximum deviation ∼±4% over the object field, so that images can be analyzed without computational corrections for the illumination pattern unless higher accuracy is desired. Custom designed detection optics produce achromatic images of the spectral region from ∼ 450 to ∼750 nm. Acquisition of a series of images of multiple fluorochromes from multiple arrays occurs under computer control. The version of the system described in detail provides images of 20 mm square areas using a 27 mm square, 2K × 2K pixel, cooled CCD chip with a well depth of ∼10(5) electrons, and provides ratio measurements accurate to a few percent over a dynamic range in intensity >1000. Resolution referred to the sample is 10 µm, sufficient for obtaining quantitative multicolor images from >30 000 array elements in an 18 mm × 18 mm square

The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary

Fluorescencein situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescencein situ hybridization and comparative mapping of the chromosomes of human, great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus) and Old World monkeys (Macaca fuscata andCercopithecus aethiops). Inversions were found in the pericentric region of the primate chromosome 2p homologs in great apes, and the hybridization pattern demonstrates the known phylogenetically derived telomere fusion in the line that leads to human chromosome 2. The hybridization of the 2q microlibrary to chromosomes of Old World monkeys gave a different pattern from that in the gorilla and the orang-utan, but a pattern similar to that of chimpanzees. This suggests convergence of chromosomal rearrangements in different phylogenetic lines

Adrift upon a salinity-stratified sea

The structure and variability of upper-ocean properties in the Bay of Bengal (BoB) modulate air-sea interactions, which profoundly influence the pattern and intensity of monsoonal precipitation across the Indian subcontinent. In turn, the bay receives a massive amount of freshwater through river input at its boundaries and from heavy local rainfall, leading to a salinity-stratified surface ocean and shallow mixed layers. Small-scale oceanographic processes that drive variability in near-surface BoB waters complicate the tight coupling between ocean and atmosphere implicit in this seasonal feedback. Unraveling these ocean dynamics and their impact on air-sea interactions is critical to improving the forecasting of intraseasonal variability in the southwest monsoon. To that end, we deployed a wave-powered, rapidly profiling system capable of measuring the structure and variability of the upper 100 m of the BoB. The evolution of upper-ocean structure along the trajectory of the instrument’s roughly two-week drift, along with direct estimates of vertical fluxes of salt and heat, permit assessment of the contributions of various phenomena to temporal and spatial variability in the surface mixed layer depth. Further, these observations suggest that the particular “barrier-layer” stratification found in the BoB may decrease the influence of the wind on mixing processes in the interior, thus isolating the upper ocean from the interior below, and tightening its coupling to the atmosphere abov

Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries

The nuclear topography of splicing snRNPs, mRNA transcripts and chromosome domains in various mammalian cell types are described. The visualization of splicing snRNPs, defined by the Sm antigen, and coiled bodies, revealed distinctly different distribution patterns in these cell types. Heat shock experiments confirmed that the distribution patterns also depend on physiological parameters. Using a combination of fluorescencein situ hybridization and immunodetection protocols, individual chromosome domains were visualized simultaneously with the Sm antigen or the transcript of an integrated human papilloma virus genome. Three-dimensional analysis of fluorescence-stained target regions was performed by confocal laser scanning microscopy. RNA transcripts and components of the splicing machinery were found to be generally excluded from the interior of the territories occupied by the individual chromosomes. Based on these findings we present a model for the functional compartmentalization of the cell nucleus. According to this model the space between chromosome domains, including the surface areas of these domains, defines a three-dimensional network-like compartment, termed the interchromosome domain (ICD) compartment, in which transcription and splicing of mRNA occurs

Mixing to monsoons: Air-sea interactions in the bay of Bengal

More than 1 billion people depend on rainfall from the South Asian monsoon for their livelihoods. Summertime monsoonal precipitation is highly variable on intraseasonal time scales, with alternating "active" and "break" periods. These intraseasonal oscillations in large-scale atmospheric convection and winds are closely tied to 1°C-2°C variations of sea surface temperature in the Bay of Bengal

A strategy for the characterization of minute chromosome rearrangements using multiple color fluorescence in situ hybridization with chromosome-specific DNA libraries and YAC clones

The identification of marker chromosomes in clinical and tumor cytogenetics by chromosome banding analysis can create problems. In this study, we present a strategy to define minute chromosomal rearrangements by multicolor fluorescence in situ hybridization (FISH) with whole chromosome painting probes derived from chromosome-specific DNA libraries and Alu-polymerase chain reaction (PCR) products of various region-specific yeast artificial chromosome (YAC) clones. To demonstrate the usefulness of this strategy for the characterization of chromosome rearrangements unidentifiable by banding techniques, an 8p+ marker chromosome with two extra bands present in the karyotype of a child with multiple anomalies, malformations, and severe mental retardation was investigated. A series of seven-color FISH experiments with sets of fluorochrome-labeled DNA library probes from flow-sorted chromosomes demonstrated that the additional segment on 8p+ was derived from chromosome 6. For a more detailed characterization of the marker chromosome, three-color FISH experiments with library probes specific to chromosomes 6 and 8 were performed in combination with newly established telomeric and subtelomeric YAC clones from 6q25, 6p23, and 8p23. These experiments demonstrated a trisomy 6pter6p22 and a monosomy 8pter8p23 in the patient. The present limitations for a broad application of this strategy and its possible improvements are discusse

Comparative chromosome painting discloses homologous Segments in distantly related mammals

Comparative chromosome painting, termed ZOO-FISH, using DNA libraries from flow sorted human chromosomes 1,16,17 and X, and mouse chromosome 11 discloses the presence of syntenic groups in distantly related mammalian Orders ranging from primates (Homo sapiens), rodents (Mus musculus), even-toed ungulates (Muntiacus muntjak vaginalis and Muntiacus reevesi) and whales (Balaenoptera physalus). These mammalian Orders have evolved separately for 55-80 million years (Myr). We conclude that ZOO-FISH can be used to generate comparative chromosome maps of a large number of mammalian species